Author Index
A
Aboussekhra, A., 625 Ainscough, R., 367 Allen, S., 767 Almouzni, G., 225 Alroy, I., 133 Anderson, K., 367 Antoniou, M., 7 Archer, T.K., 63 Arents, G., 273 Ariel, M., 307
B
Barnes, D.E., 619 Bartolomei, M.S., 287 Baum, M., 687 Beard, C., 297 Beese, L.S., 495 Bell, S.P., 435 Bellann6-Chantelot, C., 377 Benson, F.E., 525 Berks, M., 367 Berry, M., 7 Bestor, T.H., 297 Bienz-Tadmor, B., 487 Biggerstaff, M., 625 Bird, A.P., 281 Blackburn, E.H., 707 Blair, D., 367 Blow, J.J., 475 Blundell, P.A., 105 Bonaduce, M.J., 457 Bonifer, C., 37 Borst, P., 105 Botchan, M.R., 403 Bradley, J., 707 Brandeis, M., 307 Bresnick, E.H., 63 Brewer, B.J., 425 Briot, A., 645 Brown, C.J., 315 Brunkow, M.E., 287 Burley, S.K., 123
C
Canfield, T.K., 633 Carbon, J., 669 Carlson, M., 257 Carrel, L., 315 Carter, K.C., 807 Cedar, H., 307 Chapman, L., 141 Cheng, X., 331 Choy, B., 199 Chumakov, I., 377 Chung, J., 1 Cisek, L.J., 187 Clark, D., 1 Clark, K.L., 123 Clarke, L., 687 Cleary, M.A., 167 Cohen, D., 377
Collins, I., 415 Connell, M., 367 Cooper, J., 367 Cooper, J.P., 237 Corden, J.L., 187 Coulson, A., 367 Craxton, M., 367 Cremer, C., 777 Cremer, T., 777 Crothers, D.M., 115
D
Daly, G., 619 Davis, I., 793 de Boer, E., 7 Dear, S., 367 DePamphilis, M.L., 475 Dershowitz, A., 415 Deshpande, A.M., 415 Deufel, A., 505 DiBartolomeis, S.M., 487 Dietzel, S., 777 Dijkwel, P.A., 467 Di Leonardo, A., 655 Diller, J.D., 425 Dillon, N., 7 Du, W., 73 Du, Z., 367 Dujon, B., 357 Durbin, R., 367 DutnaU, R.N., 141
E
Earnshaw, W.C., 697 Egelman, E.H., 567 Elgin, S.C.R., 83 Ellis, J., 7 Emmerich, P., 777
F
Fairall, L., 141 Fang, W.-H., 597 Fangman, W.L., 425 Farkas, G., 45 Faust, N., 37 Favello, A., 367 Felsenfeld, G., 1 Ferr6-D'Amar6, A., 123 Fertitta, A., 767 Finch, J.T., 141 Forrester, W., 97 Forsburg, S.L., 637 Forster, A.C., 297 Foss, M.A., 443 Fouts, E., 403 Fox, C.A., 443 Fragoso, G., 63 Francis-Lang, H., 793 Fraser, P., 7 Freedman, L.F., 133 Friedman, J.M., 495
Friedman, K.L., 425 Fulton, L., 367
G
Gall, J.G., 747 Gallagher, R.C., 707 Galloni, M., 45 Garrett-Engele, P.W., 323 Gartler, S.M., 633 Gasser, S.M., 733 Gaszner, M., 45 Gausz, J., 45 Georgiev, G.P., 25 Gerbi, S.A., 487 Gilbert, D.M., 475 Gilson, E., 733 Gommers-Ampt, J.H., 105 Granok, H., 83 Green, M.R., 199 Green, P., 349, 367 Greenfeder, S.A., 415 Greider, C.W., 719 Griffin, L.A., 199 Gromova, I., 25 Grosschedl, R., 97 Grosveld, F., 7 Grunstein, M., 247 Guacci, V., 677 Gyurkovics, H., 45
H
Hager, G.L., 63 Hagstrom, K., 45 Hall, I., 645 Halloran, N., 367 Hamlin, J.L., 467 Hancock, R., 25 Hansen, R.S., 633 Hawkins, T., 367 Hayes, J.J., 225 Hecht, A., 37 Hecht, A., 247 Hendrich, B., 315 Henikoff, S., 577 Herr, W., 167 Hillier, L., 367 Hiom, K., 525 Hogan, E., 677 Hogga, I., 45 Holmes, J., 597 Hood, L., 339 Hurst, J., 7 Huynh, C., 367
Iarovaia, O., 25 Ikeya, T., 567 Imam, A., 7 Ish-Horowicz, D., 793
J
Jacob, F., 383 Jaenisch, R., 297 J~iger, J., 495 Jauch, A., 777 Jenuwein, T., 97 Jiang, W., 669 Jim6nez-Garcia, L.F., 799 John, S., 63 Johnston, L., 367 Jonczyk, P., 645 Jones, C.J., 625 Juan, L.-J., 213
K
Kadonaga, J.T., 205 Kafri, T., 307 Kahmann, R., 505 Kahn, J.D., 115 Kamakaka, R.T., 205 Karch, F., 45 Karzai, A.W., 389 Kelly, T.J., 637 Kelsey, G., 55 Kershaw, J., 367 Kershisnik, E.O., 577 Keshet, I., 307 Kieft, R., 105 Kim, J.L., 123 Kingsbury, J., 677 Kingston, R.E., 213 Kirsten, J., 367 Kitsberg, D., 307 Kladde, M.P., 237 Klar, A.J.S., 457 Kleckner, N., 553 Klimasauskas, S., 331 Kohlstaedt, L.A., 495 Kolor, K.M., 425 Koop, B.F., 339 Koshland, D., 677 Kozono, Y., 367 Kumar, S., 331 Kurz, A., 777
L
Laemmli, U.K., 755 Lai, J.-S., 167 Laird, C.D., 633 Laister, N., 367 LaMarco, K., 167 Lamb, M.M., 633 Lande, R., 543 Larin, Z., 55 Laroche, T., 733 Latreille, P., 367 Laurent, B.C., 257 Lawrence, J.B., 807 Learn, B., 389 Lee, E., 1 Lee, M.S., 707 LeGall, I., 377
837
838 AUTHOR INDEX
Lehmann, A.R., 619 Lehrach, H., 55 Leighton, P.A., 287 Li, E., 297 Li, G.-M., 597 L1, R., 403 Liang, C., 487 Llchter, E, 55, 777 Ligtenberg, M.J.L., 105 Lin, H.-B., 467 Lindahl, T.. 619 Linke, S.P., 655 Livanos, E., 645 Longley, M., 597 Loo. S., 443 Loughney, K., 577 Lu, H., 187 Lu, Q., 83 Luger, K., 265
M
Mackay, A.M., 697 Maniatis, T., 73 Marahrens, Y., 435 Marschall, L.G., 687 Martin-Morris, L.E., 577 Massa, H., 767 Mathieu, U., 777 McMacken, R., 389 Meijer, D., 7 Meluh, P., 677 Merker, P., 505 Miao, V., 323 Miller, A.P., 315 Miyazawa, H., 475 Mizuuchi, K., 515 Mizuuchi, M., 515 Modrich, E, 597 Montoliu, L., 55 Morse, R.H., 237 Mortimore, B., 367 Mosca, P.J., 467 Moudrianakis, E.N., 273 Mialler, H.-P., 533 Muller, M., 45 Murphy, C., 747 Murphy, M., 237 Muskhelishvili, G., 505
N
Nabetani, A., 567 Nallaseth, F.S., 475 Nash, R.A., 619 Newlon, C.S., 415 Ngan, V.K., 687 Nikolov, D.B., 123 Nurse, P., 637
O
O'Donovan, A., 625 O'Keefe, R.T., 799
Ogawa, H., 567 Ogawa, T., 567 Olson, M.V., 349 Ong, L.Y., 415 Ortega, J,M., 475
P
Palladino, F., 733 Panussis, D., 367 Patterton, H.-G., 237 Percy, C., 367 Peterson, M.G., 167 Pfeifer, K., 287 Philipsen, S., 7 Pillus, L., 733 Poortinga, G., 577 Poulose, B., 645 Prigent, C., 619 Pruss, D., 225 Pruzina, S., 7 Pryciak, P.M., 533
R
Raghuraman, M.K., 425 Rao, H., 435 Razin, A., 307 Razin, S.V., 25 Reardon, J.T., 605 Rechsteiner, T., 265 Reinberg, D., 187 Reitman, M., 1 Rhodes, D., 141 Rice, P.A,, 495 Richardson, G.A., 323 Richmond, T.J., 265 Ried, T., 777 Rifkin, L., 367 Rine, J., 443 Rinke, B., 777 Rivier, D.H., 443 Roberts, E., 619 Roberts, R.J., 331 Roberts, S.G.E., 199 Robins, R, 619 Roelofs, H., 645 Roopra, A., 367 Roth, S.Y., 237 Rowen, L., 339 Rudenko, G., 105 Rusch, K., 505
Saam, J., 287 Sachs, R., 767 Sage, M., 645 Saltoh, Y.. 755 Sancar, A., 605 Sanchez, J., 645 Satoh, M,S, 619 Saueressig, H., 37 Schafer, G., 37
Schaefer, D., 645 Schedl, A., 55 Schedl, P., 45 Scherthan, H., 777 Schrock, E., 777 Schutz, G., 55 Schwabe, J.W.R., 141 Selig, S., 307 Selker, E.U., 323 Shimizu, M., 237 Shinohara, A., 567 Shivji, M.K.K., 625 Shownkeen, R., 367 Sigler, P.B., 133 Simpson, R.T., 237 Singer, M.J., 323 Sipos, L., 45 Sippel, A.E., 37 Smaldon, N., 367 Smerdon, S., 495 Smith, A., 367 Smith, C.L., 63 Smith, H.S., 487 Smith, M.. 367 Spector, D.L., 799 Speicher, M.R., 777 Spradling, A.C., 585 Staden, R., 367 Stahl, F.W., 543 Steiner, N.C., 687 Steitz. T.A., 495 Stillman, B., 435 Strouboulis, J., 7 Strunnikov, A., 677 Studltsky, V., 1 Sulston, J., 367 Szymkowskl, D.E., 625
T
Tanese, N., 179 Taylor, I.C.A., 213 Taylor, M.C., 105 Thanos, D., 73 Theis, J.F., 415 Thierry-Mieg, J., 367 Thilly, W., 597 Thomas, J.O., 15 Thompson, J.S., 247 Thompson, L.H., 605 Tilghman. S.M., 287 Tjian, R., 179 Tlsty, T.D.. 645 Trask, B.J., 767 Treich, I., 257 Tsaneva, I.R., 525 Tsukagoshi, Y., 63 Tsvetkov, A., 747
Udvardy, A., 45 Ura, K., 225 Urnov, F.D., 487
V
van den Engh, G., 767 van Leeuwen, F., 105 Varmus, H.E., 533 Vaudin, M., 367 Vaughan, K., 367 Vazquez, J., 45 Verreault, A., 15
W
Wahl, G.M., 655 Wallrath, L.L., 83 Walter, P.P., 213 Wang, J., 495 Wang, K., 339 Waterston, R., 367 Webber, A.L., 287 Weiner, B.M., 553 Weinstock, L., 367 Wemtraub, H., 819 Weiss, A., 307 Wellinger, R.J., 725 West, S.C., 525 Westergaard, O., 25 Westphal, H., 1 White, A., 645 Whyatt, D., 7 Willard, H.F., 315 Wilson, A.C., 167 Wilson, R., 367 Wohldmann, P., 367 Wolberger, C., 159 Wolf, A.J., 725 Wolffe, A.P., 225 Wood, R.D., 625 Workman, J.L., 213 Wu, C.-H.H., 747 Wu, M., 767 Wu, N., 487 Wu, Z., 747 Wfithrich, K., 149
X
Xing, X., 807 Xu, W., 133
Y
Yamamoto, A., 677 Yang, L., 403 Yin, Y., 655 Yu, X., 567
Z
Zakian, V.A., 725 Zawel, L., 187 Zemel, S., 287 Zirbel, R., 777
Subject Index
A
37A5 antigen, 699. See also IN- CENPs
87A7, 45-48 (A)BC excinuclease, 613-614. See
also UvrABC excision repair enzymes
abd-A and Abd-B genes. See Bithorax complex
Abfl/ABF1 (ARS binding factor 1), 250, 409, 419, 436-437, 444, 448-450, 452. See also ARS
a-Cell-specific gene. See STE6 gene
Acentric structures, 656-657, 663 Acetylation of histones. See H3;
H4; Histones Achiasmatic chromosomes,
segregation, 563 ACS. See ARS, consensus se-
quence Actinomycin D, 816 Activators. See GAL4; Replication
of DNA; Transcription ADE gene, telomeric repression,
250, 733 S-Adenosyl-L-methionine
(AdoMet), crystal struc- ture with HhaI, 331-337
Adenovirus and splicing, 802, 817 Adh and positioned nucleosomes,
94 AdoMet. See S-Adenosyl-L-
methionine A element. See Lysozyme gene Alkylation tolerance and mis-
match repair, 600-601 Allele-specific gene expression,
methylation, and replica- tion timing. See Imprint- ing
c~-Amanitin, 800-801, 816 ct-Globin. See Globin genes c~-TIF. See VP16 a2 repressor
and chromatin structure in gene expression, 237-244
and retroviral DNA integration, 533, 537
Alu-PCR hybridization, YAC to YAC, for mapping, 378- 382
am gene. See Neurospora crassa 3-Aminobenzamide, 622-623 Amplifiable YACs, 55, 57-58 Amplification of DNA. See Gene
amplification; Puffs
Anaphase. See Chromosome, segregation
spindle stability and INCENPs, 697-705
Aneuploidy, 645, 650-652 Antennapedia homeodomain, 159,
163 Antp(C39S)-DNA complex,
hydration and structure, 150, 152, 155-156, 827
Antigenic variation in trypanosomes, 105-112
Antigens as chromosome pas- senger proteins, 697-705
Antimetabolites, cell cycle arrest, 659-661. See also Methotrexate; PALA
Antirepression. See Replication of DNA; Transcription
Antisense RNA pairing, 554-556 Antp(C39S). See Antennapedia
homeodomain Aphidicolin, 471,480, 599 Arab~dopsis thaliana TBP-2, X-ray
crystallographic studies, 123-126
ARS (autonomously replicating se- quence), 249, 363, 475, 477. See also Abfl/ABF1
ARS1 domains and function, 409, 435-436
ARS307 domains and function, 418-419, 435-436
consensus sequence (ACS), 418- 419, 435,444
in HM loci, 447-448 ORC binding to, 437-441
function at HMR-E, 449-450 origin interference of ARS1 and
ARS501, 428-431, 433 rDNA, 428 replication origin function, 415-
422, 425-433, 435-436 replication timing of ARS1,
ARS305, ARS501, and KEX ARS, 426-427
Assembly of preinitiation complex. See Preinitiation com- plex
Assembly of splicing complex. See Lampbrush chromosomes; Snur- posomes
Ataxia telangiectasia, 658 ATF-2 and virus induction of IFN-
[3 gene, 75-79, 834 ATP
and disassembly of preinitiation complex at orig., 389, 393
and ORC binding, 437 and transposition target im-
munity, 516, 520-522 ATPase
DNA-stimulated in SNF2, 260- 262
of RecA and Rad51 proteins, 567, 569
of RuvB protein, 526-528 A tracts in DNA bending, 115-117,
121, 538-539 att sites and retroviral DNA in-
tegration, 533-534 Autonomously replicating se-
quence. See ARS Autosomal recessive disease. See
Xeroderma pigmentosum Autosomes and imprinting, 287.
See also Imprinting 5-Azacytidine (azaC), 283, 297,
323
B
Bacterial o factors, 179, 188, 821- 822, 833
Bacteriophage k clones in mapping, 349, 351 replication in vitro, direc-
tionality and effect of transcription, 389-400, 828
repressor, 821 Bacteriophage Mu. See Phage Mu Band assignments. See
Chromosome, banding Barr body, 320, 782, 810, 831 Basal replication machinery. See
Replication of DNA Basal transcription factors and
machinery. See RNA polymerase; Transcrip- tion factors
B asic/helix-loop-helix/leucine zip- per (b/HLH/Z) form of Max, 123, 126-128
Basic pancreatic trypsin inhibitor. See BPTI
bcd gene. See Bicoid Benomyl resistance (Bml) marker.
See Neurospora crassa [3-Galactosidase. See also lacZ
expression from bluetail transposon, 52
[3-Globin. See Globin genes [3-D-Glucosyl-hydroxymethyluracil
and [3-glucosyl trans- ferase, 108-109
839
840 SUBJECT INDEX
~-Thalassemias. See Thalassemias b/HLH/Z. See Basic/helix-loop-
helix/leucine zipper form of Max
Bicoid (bcd) transcriptional activator, 258 transcript localization, 793-794
Bidirectional replication and mapping of origins. See
Mapping and unidirectional replication in
~., 389-400 Biotinylated dUTP to visualize
repair event, 626 Bithorax complex, cis-regulatory
units and pairing- sensitive elements, 48- 53
Bloom's syndrome, 621-622 bluetail transposon, 51-52 Bml marker. See Neurospora
crassa Bombyx and chromosome pairing,
560-561 "Bouquet formation," 557, 741 Bovine papillomavirus. See BPV BPTI (basic pancreatic trypsin in-
hibitor), hydration and structure, 149-150, 152- 154, 827
BPV (bovine papillomavirus) chimeric episomes and mobiliza-
tion of MMTV LTR, 63- 70
problems as model for replica- tion, 482-484
-1 replication and enhancers, 404-412
Branch migration, RuvAB- mediated, 525-530
Breakage-fusion-bridge cycle, 653, 657
Bromodomain, 259 brown gene. See Drosophila Brownian movements in inter-
chromosome domain compartment, 787-788
Budding yeast. See Yeast, Sac- charomyces cerevisiae
C
C1. See HCF CAD gene amplification, 647-652,
656, 662 Caenorhabditis elegans, genomic
sequencing and map- ping, 367-374
cAMP-binding protein (CAP), DNA bending role, 115-117
Cancer and loss of genomic integrity.
See Gene amplification and telomere length, 721-722
CAP. See cAMP-binding protein;
Catabolite activator protein
Carbamyl synthase, aspartate transcarbamylase, and dihydrooratase activity. See CAD gene amplifica- tion
Carboxy-terminal domain (CTD) of RNA polymerase II, phosphorylation of, 187, 190-197
Casein kinase II. See CKII Catabolite activator protein (CAP),
DNA bending and retroviral DNA integra- tion target, 537
C-bands, 756, 758 CBF1, 669 CBF2 gene and CBF3 suhunits,
669-675, 682 CBF5, 674 CCG1, 182, 827-828 CCGG methylation, 323 CCG repeats and methylation in
fragile X syndrome, 633- 634
cdaA1 mutants, macronuclear division and telomeric sequences, 709-711
cdc mutations, genes, and proteins cdc2-Cln kinase, 820-821 cdc2 and phosphorylation
in control of replication and mitotic checkpoint, 638, 640
RNA polymerase II, 193 CDC7 gene, 444 cdcl O+-dependent transcrip-
tional control, 639-640 CDC17 and telomere length, 720 cdc18 +, DNA replication and
coordination with mitosis, 639-642, 832
CDC46 gene, 439-440 in study of sister chromatid pair-
ing and chromosome con- densation in mitosis, 679-680
Cell cycle. See also cdc mutations, genes, and proteins; Replication of DNA
arrest by antimetabolites, 659-661.
See also Methotrexate; PALA
and DNA replication proteins, 437
in response to DNA damage. See p53; RAD proteins, RAD9
checkpoint control, 412, 683, 698, 832. See also DSC1; p53; RAD proteins, RAD9
mitotic checkpoint, 639-642 control proteins and
phosphorylation, 193, 638, 640
coordination with replication, 384-386, 487, 637-642. See also Replication of DNA, timing
S phase, 439, 441, 444 and chromosome breakage,
657 nuclei in CHO cells and
Xenopus extracts, replication initiation, 479-481
premeiotic vs. mitotic, ARS element role, 421
replication timing of ARSs, 426-427
-specific genes, 638-640 Cell membrane and replication
control, 384-385 cen/ CEN locus, 669-675, 682,
687-694. See also Centromere
CENP-E, 699, 704-705. See also INCENPs
Centromere, 421,432, 563-564. See also Genomic se- quencing; INCENPs
and ARS308, 428 assembly and function in S.
cerevisiae, 681-683 CBF3 subunits and function in
S. cerevisiae, 669-675, 682
conditional, for amplifiable YACs, 55, 57
and FISH effect on nuclear to- pography, 781-782
gene conversions at, distribution of exchange models, 545-550
heterochromatin, 756, 758 position effects in S. pombe, 249 structure, function, and K
repeats in S. pombe, 687-694
CFF. See HCF CFP (circular form of plasmid) and
yeast telomere replica- tion, 727-730
Chiasma interference, 543-550 Chicken globin genes, chromatin
structure, 1-3, 15-22 Chicken INCENPs, 697, 699-705 Chicken lysozyme locus, 3, 37-43,
823 Chicken RAD51 gene, 573-575 Chimerisms in YACs, 377-379 Chinese hamster ovary (CHO)
cells complementation groups and ex-
cision repair, 605-615 S-phase nuclei, replication in-
itiation, 479-481 CHO cells. See Chinese hamster
ovary cells
SUBJECT INDEX 841
Chromatid interference, 543 Chromatid pairing and attach-
ment. See Sister chromatids
Chromatin. See also Acentric structures; Heterochromatin; Histones; Loops; Nucleosomes; scs and S C S t
assembly and replication, 233, 408-409, 411-412
and nuclear organization, 478- 482, 484
compacting in nucleus, structure and organization, 1, 15- 22, 45, 83, 92, 94, 248, 273-275, 692-694, 758, 782, 810. See also DNA; Domains; Heterochromatin; Nucleosomes; Scaffold
10-nm fiber, 22, 63, 254 30-nm fiber, 1, 15, 22, 45, 63,
130, 248, 758, 810 and electric forces of inter-
chromosome domain compartment, 786-788
and imprinting defect, 461,463 in interphase, 247-248, 771-
772, 774 movements within nucleus, 788-
789 and nuclear membrane interac-
tion. See Nuclear en- velope
nuclease sensitivity. See DNase I sensitivity of chromatin
structure alterations by SNF/SWI
proteins, 262 and centromere function, 692-
694 (CT) n elements, 89, 94 and DNA repair, 623, 630 effect on retroviral DNA in-
tegration, 533-540 effect on transcriptional com-
petence and control. See DNase I sensitivity of chromatin; Domains; Transcription
effect on transcription factor access to binding sites. See Transcription factors
of H19 imprinted gene and DNA methylation, 289- 291, 293, 311
HMG I(Y) role in, 79 mapping, 84-85 -mediated transcription
repression. See Tran- scription, repression and silencing
preset gene configuration vs. remodeling, 83, 88
hsp26 as preset gene, 83-95 and X inactivation, 320
and transcript export, 794-796 Chromatosome-like complexes of
Hi on nucleosome cores, 214, 217, 221
Chromomycin, 29 Chromosomal control elements
and X inactivation. See Chromosome, X
Chromosomal in situ suppression hybridization. See CISS hybridization
Chromosomal origin of replication. See Mapping; Replica- tion of DNA
Chromosome. See also Centromere; DNA; Mini- chromosomes; Telomere; YACs
7 (mouse) imprinted genes. See H19
gene; Igf2 and receptor genes; snRNA and snRNPs
tyrosinase gene, 55-56 21 (human), physical mapping,
377-382 I, II, III (S. pombe) centromere,
687-694 III (C. elegans), sequencing,
367-374 III (yeast), 248
ARS elements, replication origin function. See ARS
sequencing and mapping, 357- 359, 362-365
IV (yeast), ARS1, 426-431, 433 V (yeast)
ARS501, 426-433 replication terminus, 431
XI (yeast), sequencing and map- ping, 357-362
XIV (yeast), KEX2 ARS, 426- 427
achiasmatic, chromosome segregation, 563
arrangements, cell-type-specific, 788-789
autosomes and imprinting, 287. See also Imprinting
banding by FISH, 768 and SARs, 755-764
breakage and gene amplifica- tion, 656-657. See also Gene amplification
condensation, 703-704, 782 failure and breakage. See
Fragile X syndrome and loop/scaffold model. See
Loops for mitosis, 680-681,697 at time of homologous pairing,
562 cytogenetic analysis of ab-
normalities by FISH, 772-774
dicentric, 652-653, 656-657, 663 domains and structure. See
Chromatin; Domains double minute (DMs), 656-657,
663 interphase and metaphase, map-
ping, 767-774 lampbrush, 45, 747-749, 752 pairing of homologous, unstable
interactions in, 553-564 passenger proteins, 697-705 polytene, 45,487, 491,544 rearrangements. See Deletions;
Dicentric chromosomes; Duplication; Gene amplification; Inver- sions; Mating-type inter- conversion; Retroviral DNA integration; Trans- locations; Transposition
segregation, 385-386, 549, 563, 677, 680-681, 697-698, 705. See also Centromere; INCENPs; Kinetochore; Mitotic spindle and spindle pole bodies; Strand- segregation model
site-specific replication initia- tion, 475-484
-specific sublibraries for map- ping human genome, 379-380
territories. See Domains X
dystrophin gene chromatin condensation, 810 localization, 782-784, 808
fragile sites (fragile X syndrome), replication timing and methylation, 633-634, 832
inactivation, 311,315, 782 epigenetic and chromosomal
control of gene expres- sion, 315-321, 831
inactivation center (X/C), 315, 318-321
and methy]ation, 282, 312, 319, 831
and replication timing, 307- 308, 311
and X/ST /X i s t gene, 294, 303, 317-321,831
X (Drosophila), chiasma inter- ference and linkage map distance, 543-550
Y (Drosophila), imprinting and position-effect variega- tion, 593-594
Y (human), 381-382 STS-content mapping,
resolution-completeness profile, 352-353
842 SUBJECT INDEX
Ciliate telomerase, 707-717, 719- 720, 725, 832
Circle-to-circle replication. See Replication of DNA
cis-Acting elements and expression of homeotic
genes, 48-53 for lysozyme gene, 37, 39-42
"concerted action model" for transcription regulation, 38, 42-43
and replication timing, 307, 311 and silencing of mating loci,
248-249 and silencing of trypanosome
genes, 107-108 and transcription, 32
cis-Limited inactivation in X chromosome. See Chromosome, X
CISS (chromosomal in situ sup- pression) hybridization, 779, 782-784
CKII (casein kinase II), 619, 621 Cleavage furrow, 697-700, 705 Clonal evolution model of
tumorigenesis, 655 Clonal position effects. See Gene
expression Clone fingerprinting and overlap.
See Mapping Cloning large DNA fragments. See
YACs Coactivators of transcription and
TAFs, 179-184, 202 Cockayne's syndrome (CS) and ex-
cision repair, 606, 612- 613, 63O
Coefficient of coincidence, 543- 544, 547, 549-550
Coiled bodies, 785-786, 813 and RNA processing, 749-753
Coilin and related proteins, 749, 752-753
ColE 1 antisense RNA pairing, 555-556
Colocalization of homologous chromosomes, 553-564
Comparative genomic hybridiza- tion (CGH), 646
Complementation groups and exci- sion repair, 605-615, 625-631
Concerted evolution. See Evolution Condensation of chromatin and
chromosomes. See Chromatin; Chromosome
Confocal microscopy, 782-785, 789. See also Chromosome, banding, and SARs
Conservation of sequence. See Evolution
Constant (C) region of TCR. See TCR
Contigs. See Mapping
Conversion. See Gene conversion Copy number. See also Compara-
tive genomic hybridiza- tion
dependence. See Gene expres- sion; Methylation of DNA
increase. See Gene amplification regulation in transposons, 592-
594 Core histones. See H2; H3; H4;
Histones, octamer Core promoter element, 123, 187.
See also TATA box Cosmid clones in mapping and se-
quencing. See Genomic sequencing; Mapping
CP1,669 CpG methylation. See Methylation
of DNA CpG to TpG transitions, 622 C (constant) region of TCR. See
TCR Cross-linking
histone/DNA, 226-227, 267 interstrand, by mitomycin C,
612 pyridoxyl 5 r phosphate to
reverse transcriptase and Klenow fragment, 497-498
UV-mediated H1 and MMTV LTR promoter,
65-67 H5/DNA in ~-globin, 15-22
Crossovers accompanying gene conversion.
See Chiasma inter- ference
and homologous chromosome pairing, 556
Crystal-packing effects on protein surface, 149
Crystal structure. See X-ray crys- tal structure
CS. See Cockayne's syndrome and excision repair
CT-binding protein. See GAGA fac- tor
CTD. See Carboxy-terminal domain of RNA polymerase II
(CT) n elements, role in transcrip- tional activation, 89, 94
CTF13, 674 Cyclization kinetics and DNA
bending, 115-122 Cys2-His 2 and Cys2-Cys 2. See Zinc
fingers and zinc- stabilized motifs
Cytogenetic analysis in interphase and metaphase chromosomes by FISH, 772-774. See also Chromosome, banding
Cytokinesis and INCENPs, 697- 705
Cytoplasmic localization of pair- rule transcripts. See Drosophila
Cytosine methylation. See Methylation of DNA
Cytoskeleton and chromosome passenger proteins, 698, 703
D
dam methylase and replication control, 384-385 in study of yeast chromatin
structure, 251 Daunomycin staining of
chromosome bands and SARs, 756, 758-764
Debye-Hfickel forces on chromosome territories, 787-788
D (diversity) gene segment. See TCR
Deletions, FISH for cytogenetic analysis, 772-773
De novo methylation, 283, 324- 325, 328
Deoxyadenosine methylation. See dam methylase
DHFR (dihydrofolate reductase) locus, 664
and gene amplification, 648, 651, 657
replication initiation in, 467- 472, 476-477, 480, 488
Dicentric chromosomes, 652-653, 656-657, 663
Dihydrofolate reductase. See DHFR locus
Directionality of replication fork movement and 2-D gel anal-
ysis of replication inter- mediates. See Mapping
k, 389-400 Distamycin, 28 Diversity (D) gene segment. See
TCR Dmcl, 573-575 DMs (double minute
chromosomes), 656-657, 663
DNA. See also Chromosome; Cross-linking; Genomic sequencing; Loops; Map- ping; Methylation of DNA; Minicircle DNA
amplification, intra- and ex- trachromosomal, 487. See also Gene amplifica- tion; Puffs
attachment to nuclear matrix. See MARs; Scaffold, -associated regions
bending, 65, 78, 505
SUBJECT INDEX 843
A tracts in, 115-117, 121,538- 539
free energy of, 120-122 and HMG I(Y), 75, 79 mechanisms, 115 and retroviral DNA integra-
tion target at major groove, 537-539
and synergistic action of tran- scription initiation proteins, 115-122
-binding proteins. See c~2 repres- sor; Catabolite activator protein; DNA, bending; Domains; Enhancer; GAGA factor; GAL4; HhaI crystal structure; Histones; Homeodomain proteins; lac repressor; LexA; ORC; PARP; Rapl/RAP1; RecA; RNA polymerase; RPA; RuvABC proteins; Tran- scription factors; Zinc fingers and zinc- stabilized motifs
cleavage. See DNase I sensitivity of chromatin; Double- stranded DNA break; Recombination; Topoisomerase
cloning large fragments. See YACs
compacting in nucleus. See Chromatin
concerted evolution of double helix and core histones, 278
damage and cell cycle arrest. See p53;
RAD proteins, RAD9 and repair. See Repair of DNA
domains and structure. See Chromatin; Domains; Heterochromatin
electrostatic charge and hydra- tion in compaction of double helix, 274
fragile sites. See Fragile X syndrome
gapped, 525, 528-529. See also Recombination; Repair of DNA
hydration water in recognition, 155-156
incision mechanism, 626-628 insertion. See Retroviral DNA
integration; Transposi- tion
invertase. See Inversions joining. See DNA ligases; PARP;
Repair of DNA modified nucleoside in silencing
ofVSG gene, 108-109 nicked circular, RNA polymerase
binding to, 118-122
nicking and transcription sensitivity, 32
rearrangements and elimina- tion. See Genome, stability
-stimulated ATPase in SNF2, 260-262
strand exchange or transfer. See Recombination
supercoiling, 274 and Gin/FIS-mediated recom-
bination, 505-506, 511 and replication templates. See
Bacteriophage k; BPV and RNA polymerase binding,
120 and transcription, 4, 32
synthesis. See Replication of DNA; Telomere, and telomerase
telomeric, 707. See also Telomere
transcription factor access to. See Transcription factors
-typing screen for brown + dele- tions. See Drosophila, brown gene
unwinding. See DNA helicase; Topoisomerase, II
element (DUE), 419 and strand exchange. See
Recombination dnaA protein. See Replication of
DNA DnaB protein. See DNA helicase DNA-dependent RNA
polymerases. See RNA polymerase
DNA fluorochromes in chromosome banding, 756-764
DNA helicase, 398, 630, 717. See also Mismatch repair
DnaB and k replication, 389- 390, 397-398, 400
El, 405-406, 411-412 of ERCC proteins, 629-630 and excision repair, 629-631 -like domain of SNF2, 259-260 of RuvAB, 527-528 T antigen, 411-412 of TFIIH, 193, 197, 262
DnaJ and DnaK. See Heat shock genes
DNA ligases, I, II, and III, 619- 622
DNA methyltransferases. See Methyltransferases
DNA polymerases, 725 accessory factor. See PCNA a, 642, 720
inhibitor. See Aphidicolin :primase, 412, 637
5 or e, 615, 626, 629, 631,637 III holoenzyme
subunit ofE. coli, 629
and ~. replication. See Bac- teriophage
and repair. See Mismatch repair
reverse transcriptase and Klenow fragment, mechanism, nucleo- tide misincorporation, and structure, 495- 5O3
DNA primase. See Primase DNA puffs. See Puffs DNase I sensitivity of chromatin,
37, 248, 437, 550 hypersensitivity regions, 37, 51,
83 in centromeric repeat, 693 gene remodeling to form, 83 in globin, 1-3, 5, 7, 18, 21,822 in hsp26, 87
role of (CT) n elements, 89 and insulator elements, 3, 22,
32, 45-48 in lysozyme gene, 37, 39, 42 MARs and cryptic promoters
in generating, 97-102 in M A T loci, 250 in regulation of replication and
transcription, 492 and retroviral DNA integra-
tion targets, 534, 537, 539
and steroid-receptor binding to nucleosome B, 63-64, 66
and topoisomerase II, 26-28 in regulatory unit for lysozyme
gene transcription, 38- 39, 42
and transcriptional competence of ~-globin domain, 15- 22
DNA topoisomerase. See Topoisomerase
Domains a-globin, 25-26, 31 ARS1, 435-436 ARS307, 418-419, 435-436 ~-globin, 15-22 border regions in lysozyme gene,
37-39, 41-42 bromodomain, 259 of chromatin structure for
repression of yeast genes, 237-244
linkage to replication initia- tion, 452-454
of chromosome, functional com- partmentalization of nucleus, 777-789
transcript domains and splic- ing, 799, 813-817
coiled-coil and INCENP binding to micro-
tubules, 697, 700, 705 of lamins A and C, homology
with SIR4, 743-744
844 SUBJECT INDEX
Domains (continued) communication within and be-
tween, 33 containing rRNA genes,
26-29 containing single-copy genes,
29-31 DNA-binding, in steroid recep-
tors and transcription factors, 123-130, 133- 139, 141-146, 826-827. See also Homeodomain proteins; Zinc fingers and zinc-stabilized motifs
of DNA ligases, 619-621 of DNA methyltransferase, 297 DNase-sensitive chromatin,
regulatory unit for lysozyme gene transcrip- tion, 37-43
domain fragments for use in YACs, 31-32
and enhancer trapping, 795 helicase-like, SNF2, 259-260 of histone amino terminus, tran-
scription repression, 238, 252
of HMR-E silencer, 444 oflgf2-H19, allele-specific struc-
tures in, 307-312 in interphase nuclei, 771 joint-pairing. See Chromosome,
pairing of homologous ligand-binding, in steroid recep-
tor, 133 methylation, allele-specific, 289-
294 positive regulatory (PRDs), IFN-
gene, 73-80 POU, 169. See also Oct-1 and
Oct-2 homeodomain proteins
in protein/protein interactions of Gin/FIS-mediated recombination, 505-512
putative boundary elements 87A7 heat shock locus, 45-48.
See also scs and scs ~ bithorax complex, 48-53
in recombination/repair proteins, 569, 574-575
and replication control, 32 activation, 404, 409-411 timing and allele-specific ex-
pression, 307-308, 310- 311
RNA polymerase II carboxy- terminal, 187, 190-197
Smclp and NTP-binding motif of mechanochemical motors, 681
and subdomains of reverse transcriptase and Klenow fragment, 495- 498, 5O3
target recognition, HhaI, 331, 334-335
templating, of telomerase RNA, 715-716
topological organization and zeste protein, 33
and transcription control, 32-33, 37
activation, 167-169, 171, 179- 181, 183, 199, 822, 825
alleviating nucleosome- or HI- mediated repression in GAL4 derivatives, 213, 220-222
in yeast centromeres, 669, 682- 683, 687
Dominant variegation, 577. See also Drosophila, brown gene
Donnan potentials and chromosome territories, 788
Double minute chromosomes (DMs), 656-657, 663
Double-stranded DNA break (DSB), 550, 659
and cell cycle checkpoint control, 657, 832
imprinting event in mating-type interconversion, 458-464
joining. See DNA ligases; PARP. See also Repair of DNA
and recombination. See Recom- bination
Drosophila, 591, 829, 833. See also GAGA factor; Heat shock genes; Heterochromatin; Homeodomain proteins; Homeotic genes; In- sulator elements; P ele- ment
brown gene, trans-inactivation and dominant variega- tion, 577-583, 822
chorion gene and amplification, 487-488, 490, 492
DNA ligase I in, 619 enhancer-trap transposons. See
Enhancer, trapping and excision repair, 611 and pairing of homologous
chromosomes, 553 pairing-sensitive elements and
cis-regulatory units, 48- 53
pair-rule transcript localization and export, 793-797
Tramtrack, 141-143, 146 transvection and domain com-
munication, 33 white gene, 359
and enhancer blocking, 47-48 pairing-sensitive repression,
52-53 position effect of reporter gene
in euchromatin, 46
and topological organization of domains, 33
variegating phenotype in heterochromatin, 84, 93- 95, 247, 577
X chromosome, chiasma inter- ference and linkage map distance, 543-550
Y chromosome, imprinting and position-effect variega- tion, 593-594
yellow gene, genomic instability and position-effect variegation, 585-590
DSB. See Double-stranded DNA break
DSC1 (or MCBF), 638-639, 679- 680, 683
DUE (DNA unwinding element), 419
Duplication FISH for cytogenetic analysis,
772-773 in retroviral DNA integration,
533 Dystrophin gene
chromatin condensation, 810 localization, 782-784, 808
E
E-box recognition by transcription factors, 127-128
E1 helicase. See DNA helicase E2 and E1 in replication, 404-412 E2F, 664 EBV (Epstein-Barr virus), nuclear
RNA tracks, 784-785, 811,815
Ecdysone, role in transcription and DNA amplification, 488, 491-493
Electric forces acting on chromosomal territories, 786-789
Electron microscopy to visualize repair event, 626
Electrophoresis. See Mapping Electrostatic charge in compaction
of double helix, 274 Elongation. See also Processivity
cycling with transcription initia- tion, role of RNA polymerase phosphory]a- tion, 187-197
inhibitor. See Aphidicolin Embryonic development and
methylation. See Im- printing; Methylation of DNA
Endonuclease for dual incision in excision repair, 627
Engrailed homeodomain, 159, 162-163
Enhancer, 123, 821-822. See also
SUBJE CT INDEX 845
Gene expression; Tran- scription
-binding factors in antirepres- sion, 210-211
-binding HNF-3/fork head, 124, 128-130
blocking, 47-48, 52 cell-stage specific activation in
myeloid cells, 39-40 in Gin/FIS-mediated recombina-
tion, 505-506, 511 and globin LCR, 1-3, 5, 18, 822-
823 immunoglobulin K, 346 and imprinting of H19 and Igf2
genes, 288, 291,293-294 and looping, 823 in ]ysozyme cells, 42 ~, and factor access in
chromatin, 97-102 in replication initiation in BPV-
1,403-412 sequences in TCR loci, 346 structural role of proteins in
function of, 78-79 TCR-a gene, 78 and topological organization of
domains, 33 trapping, 586, 590, 795-796 virus-inducible complex of IFN-~
gene, HMG I(Y) and combinatorial control, 73-80, 834
Epigenetic inheritance and con- trol, 444-445, 829-832. See also Chromosome, X; Imprinting; Transcrip- tion, repression and silencing
Epipodophyllotoxin. See VM-26 Episomal replication. See ARS Episomes, 656, 663 e-Globin. See Globin gene switch-
ing Epstein-Barr virus. See EBV ERCC (excision repair cross-
complementing) genes and proteins, 606, 609, 611-613, 625-631
Erythroid cells, 1, 37. See also Globin gene switching; Globin genes
ESAGs. See Expression-site asso- ciated genes
Escherichia coh enzymes, genes, and proteins.
See dam methylase; Heat shock genes; HU protein; Klenow frag- ment of DNA polymerase I; lacZ; LexA; RNA polymerase
in recombination/repair, 597- 598. See also (A)BC ex- cinuclease; FIS; mfd gene product; RecA;
RuvABC proteins; Uv- rABC excision repair en- zymes
oriC. See Replication of DNA, origin
E silencers, 444. See also HM loci and repression
EST1 and telomerase, 720 Estrogen receptor
DNA-binding domain, 133-139, 141,143-146
in transcriptional activation and regulation, 94
Ethidium bromide, 118, 756 Euchromatin, 46, 84, 247, 577,
585-594, 758, 782. See also Chromatin
Euplotes telomerase, 707, 719 Evolution
concerted, 347 for double helix and core
histones, 278 and conserved sequences in C.
elegans, 373 of heterochromatin, transposon
role, 594 TCR loci in mouse and human,
343-346 trypsinogen gene, 346-347
Excinuclease (excision nuclease) in DNA repair, 605-615
Excision (bidirectional) in mis- match repair, 597-600
Excision and gap repair, 528, 578, 581,598, 625-631
human/rodent excision nuclease and excision assay, 605- 615
PARP role, 622-623 Excision of transposons, 593 3 ' ,5 ' -Exonuclease activity of
Klenow fragment, 495, 499-502
Exonuclease in mismatch repair, 597-598
Export of transcripts. See Nucleus Expression of genes. See Gene ex-
pression Expression-site associated genes
(ESAGs), 110 Extrachromosomal elements and
chromosome breakage, 656-657, 663
e(y) genes and zeste protein, 33
F
Fab-7, 51-52 Fibrillarin, 750, 752-753 Fibronectin RNA, 811-813, 815-
816 Fibrous corona, 675 Fingerprinting. See Mapping FIS, Gin-mediated recombination
and genetic mapping, 505-512
FISH (fluorescence in situ hybridization), 784
for banding assignments, 768 for cytogenetic analysis of
chromosomal ab- normalities, 772-774
in localization of RNA tracks, 810-813
in mapping human genome using YAC contigs, 377- 379, 382
in mapping metaphase and in- terphase chromosomes, 767-774
in measuring chromatin con- densation, 810
and nuclear topography, 781- 782, 789, 808-810
replication patterns of lgf2-H19 region, 307-308
technique, 767-768 for YAC DNA integration in gen-
erating transgenic mice, 58-59
for yeast chromosomes in mitosis, 678-681
for yeast meiotic chromosome pairing, 553-554
Fission yeast. See Yeast, Schizosaccharomyces pombe
Flow cytometry in measuring amplification fre-
quency, 648, 651 and ORC role, 439
Fluorescence in situ hybridization. See FISH
Fluorochromes. See also FISH in chromosome banding, 756-
764 Footprinting
on DNA-binding surface of histone octamer, 276- 277
of MuB at transposition target, 520-521
nucleosome cores, 65 Fragile X syndrome, replication
timing and methylation, 633-634, 832
FRAXA. See Fragile X syndrome Free energy of DNA bending, 120-
122 ftz. See fushi tarazu fushi tarazu, 795
transcriptional regulator. See Tramtrack
Fusion-bridge-breakage cycle, 653, 657
G
GAGA factor, role in transcription, 85-86, 89, 91, 94-95, 205-207
846 SUBJECT INDEX
GAL4 derivatives and transcriptional
activation/reactivation, 180, 200-201,213-222
GAL4-VP16, 206-207, 209- 211,213-214, 219-222
LexA-GAL4 fusion protein, 437
and function of SNF/SWI proteins, 258
and DNA replication, GAL4- p53(1-73) and GAL4- VP16, 409-412
y-Globin. See Globin gene switch- ing
y-Irradiation and DNA damage. See p53
Gapped DNA. See DNA; Repair of DNA
GATA1, 8 G-bands, 756, 758 GC periodicity in yeast
chromosomes, 363, 365 Gel electrophoresis. See Mapping Gene amplification
FISH for cytogenetic analysis, 772-774
as genetic instability marker, 645-653, 655-665
Gene conversion. See also Chiasma interference; Drosophila, brown gene; Mating-type interconver- sion
in yeast telomeric DNA replica- tion, 725, 731
Gene disruption in yeast chromosomes, 359, 364
Gene domain transfer, 40-43 Gene expression, 33. See also
Transcription allele-specific and developmen-
tal regulation. See Im- printing
and DNase sensitivity. See DNase I sensitivity of chromatin
and enhancer trapping. See En- hancer, trapping
epigenetic control, 829-832. See also Chromosome, X; Im- printing; Transcription, repression and silencing
and genome organization, 808, 815-816
globin chromatin structure role, 1-5,
15-22 copy number dependence, 7 developmental regulation and
gene switching, 7-12 position independence, 3, 7-10
homeotic genes in bithorax com- plex, 48-53, 788
hormone inducible. See Estrogen receptor; Glucocorticoid
receptor; Progesterone receptor; Steroid recep- tor
immediate early. See VP16 and interchromosome domain
compartment, 786-788 long-range control. See Enhan-
cer; Insulator elements; LCR; Transcription
lysozyme control by chromatin
regulatory units, 37-43 position effects and copy num-
ber dependence, 41-43 methylation role. See Methyla-
tion of DNA mouse RAD51 gene, 575 pairing-sensitive repression, 52-
53 position effect of reporter gene
integration, 37, 46 position-effect variegation. See
Heterochromatin preset genes vs. remodeling, 83,
88 hsp26 as preset gene, 83-95
recombination in regulation. See Recombination
regulation of genes for DNA replication, 638-639
repression and silencing. See Transcription, repres- sion and silencing
segmentation genes, 48-53, 793- 794
and "trans-sensing effects," 577 tyrosinase (YAC-borne), copy-
number dependence and position independence, 56, 60
virus inducible in IFN-[~, 73-80 X-linked. See Chromosome, X yeast, 437, 441,585, 829-830
a-cell- or mating-type-specific. See a2 repressor; HM loci and repression
chromatin structure in tran- scription repression and replication, 237-244, 250-255, 443-444, 450- 454, 743-744
copy number of S1R4 gene and HM repression, 738-740
and coupling replication to cell cycle, 638-639
position effects, 248-250, 253- 254, 421-422, 427, 443- 444, 733, 743-744
SNF/SWI proteins in, 257-262 Gene-gating model of export, 794-
796 General transcription factors
(GTFs). See Transcrip- tion factors
Gene replacement. See Antigenic variation in
trypanosomes Gene switching. See Globin gene
switching; Mating-type interconversion
Genetic complementation groups. See Complementation groups and excision repair
Genetic distance and chiasma in- terference, 543-550
Genetic mapping. See Mapping Genome
integration of structure with RNA metabolism, 807- 817
mapping and analysis. See Map- ping; YACs
methylation density, 281-283 stability, 832. See also
Aneuploidy; Deletions; Chromosome, X; Dicentric chromosomes; Duplication; Gene amplification; Inver- sions; Mating-type inter- conversion; Transloca- tions
and cell cycle checkpoint con- trol. See Cell cycle
integration of DNA into. See Heterochromatin; Retroviral DNA integration; Transposition
and mismatch repair, 597-602 SIR3, SIR4, and RAP1 in, 734,
740-741,744-745 Genomic imprinting. See Imprint-
ing Genomic sequencing, 835
of C. elegans, shotgun and directed strategies, 367- 374
large-scale comparative analyses of mouse and human TCR loci, 339-347
ofNeurospora, methylation, 323, 328
ofS. cerevisiae, 357-365 and transcript mapping of brown
gene, 578-580 Germinal vesicle (GV) of
amphibian oocytes. See Xenopus
Giemsa staining of chromosome bands and SARs, 756, 758-759, 763
Gin/FIS-mediated site-specific recombination, genetic mapping of interaction domains, 505-512
gix inverted repeat, 505-506 Globin genes
a-globin, 25-26, 31 ~-globin. See also LCR
chromatin structure and
SUBJECT INDEX 847
DNase I sensitivity, 15- 22
gene domain and replication timing in Igf2-H19, 307, 311
insulator element, 3, 823 chromatin structure role in ex-
pression, 1-5 developmental regulation of ex-
pression. See Globin gene switching
Globin gene switching, 7-12 Glucocorticoid receptor, transcrip-
tional activation and regulation, 64, 68, 825. See also Steroid receptor
DNA-binding domain, 133-139, 143-146
Glucosyl transferase and VSG gene, 108-109
Glycoprotein (surface) gene of trypanosome, 106-112
G6PD and X inactivation, 316-317 GrpE. See Heat shock genes GTFs (general transcription fac-
tors). See Transcription factors
GV (germinal vesicle). See Xenopus
gypsy, 3, 52
H
H1, 5, 15, 18-22, 69, 130, 193, 233-234, 248, 680, 825. See also Histones
association in nucleosome struc- ture, 217, 228-232, 265- 266, 270-271
cross-linking assay and MMTV LTR promoter activa- tion, 65-67
and factor access to nucleosomal DNA, 217-218, 233-234
-mediated repression, 94, 206- 222, 825
and SARs, 79, 755 H2, octamer structure, 265, 267-
270, 275-279. See also Histones
H3. See also Histones acetylation, 253 octamer structure, 265-270,
275-279 and regulation of silencing in
yeast, 252, 824 H4, 83, 733. See also Histones
acetylation, 247-248, 251-253 in chromatin structure, a-cell-
specific gene expression, 238-239
octamer structure, 265-270, 275-279
and regulation of silencing in yeast, 252-254, 443, 824
H5, 5, 15. See also Histones
globular domain structure, 130 H5/DNA interactions in ~-globin
domain, 17-22 H19 gene, 287,831
Igf2-H19 domain, differential replication timing and allele-specific expres- sion, 307-312
methylation and imprinting, 282, 287-294, 297-298, 300-301, 303-304, 309- 312
hairy (h) gene, 795-796 Handshake motif of histone oc-
tamer, 276 Haploid mating function, 248 Haploid-specific genes, repression
of, 241 HCF (host-cell factor), structure
and role in Oct-1/VP16 association, 169-176
Heat shock genes Drosophila
87A7, putative domain bound- ary elements, 45-48
hsp26 as preset gene, chromatin structure role in expression, 83-95
hsp70 insulator elements. See scs and scs '
E. coli, DnaJ, DnaK, and GrpE in ~. replication in vitro, 389-400
Helical repeats and discontinuity of nucleosoma] core DNA, 226, 228, 231-232
Helicase. See DNA helicase Helix-loop-helix (HLH) transcrip-
tion factors, 126-127. See also Basic/helix-loop- helixfleucine zipper form of Max; Transcription factors
Helix-turn-helix (HTH) motif in FIS, 505 in homeodomains, 159, 161, 169
Hematopoietic system. See Erythroid cells; Macro- phages; Myelomonocytic lineage
Hepatocyte nuclear factor-3),. See HNF-3/fork head
Herpes simplex virus VP16. See VP16
Heterochromatin, 247-248, 443, 733, 735, 743, 788
histone role in repression of gene expression
Drosophda, 247-248 yeast mating-type, 250-255
and LCR function, 3 of loop base and chromosome
bands, 755-756, 758 and pairing of sister chromatids,
679 and variegating phenotype, 92-
95, 247, 250, 577 dominant variegation and
trans-inactivation of brown gene, 577-583, 822
role of genomic instability and transposable elements, 585-594
trans-acting repressors of variegation and heterochromatin dosage, 593
and X inactivation, 320, 782 Heterodimers and combinatorial
control, 833 Heteroduplex joint. See Holliday
junctions Heterogeneous nuclear RNA
(hnRNA). See Poly(A) RNA and pre-mRNA me- tabolism
HhaI crystal structure, 331-337 1H-1H nuclear Overhauser effects.
See NOEs High mobility group proteins. See
HMG-1; HMG I(Y) Histones, 4-5, 63, 115, 623, 680.
See also Chromatin; H1; H3; H4; H5; Nucleosomes
acetylation, 232-233. See also H3; H4
role of Sir2, 253-254 amino-terminal tails, 265,267-
270, 277 and factor access, 225, 227-
228, 232-233 and repression at silent
mating loci and telomeres, 252-253
competitors and nucleosome dis- placement, 222
concerted evolution of core and double helix, 278
cross-linking to DNA, 226-227, 267. See also H1
dimer/tetramer interface, 278- 279
fold, handshake motif, labile termini, protein super- coil, and parallel !3 bridge and paired ends of helices motifs, 276- 279, 827
genes and methylation, 282-283 -like protein. See HU protein linker, 15-22, 130, 225, 228-231.
See also H1; H5 octamer, 45, 228, 233, 273,405,
408-409, 475 core position for translation,
226-228, 231-232 structure and function, 265-
271, 273-279 and retroviral DNA integration
targets, 537
848 SUBJECT INDEX
Histones (continued) role in transcription regulation
and chromatin structure, 242-244, 825-826. See also H4
factor access, 102, 225-234 repression by
heterochromatin, 247- 248, 250-255
tetramer, 226, 228, 232-233, 252, 267, 275-276, 278- 279
transcription of genes and pre- mRNA processing, 747, 749, 752-753
HIV (human immunodeficiency virus). See also Reverse transcriptase
integrase, 535, 537-538 HLH. See Helix-loop-helix tran-
scription factors HMG-1, 74-75 HMG I(Y)
and binding to SARs, 79, 755, 763
role in virus induction of IFN-~ gene, 74-80, 834
HM loci and repression, 248-255, 421,437, 733, 737, 740, 743-744, 829-830. See also Sir/SIR proteins
linkage to replication initiation, 443-454
HNF (hepatocyte nuclear factor)- 3~fork head, X-ray crys- tallographic studies, 124, 128-130, 826-827
hnRNA (heterogenous nuclear RNA). See Poly(A) RNA and pre-mRNA metabo- lism
HO endonuclease accessibility, SIR-dependence, 450- 452
Holliday junctions, branch migra- tion and resolution, 525- 530
Homeodomain proteins Antennapedia, 159, 163
Antp(C39S)-DNA complex, 150, 152, 155-156
engrailed, 159, 162-163 MAT(~2, 159-165 Oct-1 and Oct-2, 167-176
Homeotic genes, 247, 788, 823, 831 in bithorax complex, 48-53 fork head, 128
HOM homeobox cluster in C. elegans, 370
Homologous recombination of DNA methyltransferase gene.
See Methyltransferases for inserting I-Sce I sites. See I-
Sce I sites Homology
in C. elegans sequence, 370
-dependent chromosome pairing, unstable interactions in, 553-564
in DNA ligases, 619-621 in excision repair genes. See
Complementation groups and excision repair
in human/mouse TCR loci, 343- 346
to RecA proteins, 567, 569, 573- 575
in telomeric sequences, 707-708, 719
and yeast orphan genes, 359, 361
Hormone receptors in transcrip- tional activation and regulation, 73. See also Estrogen receptor; Glucocorticoid receptor; Progesterone receptor; Steroid receptor; Thyroid hormone receptor
Hormone response elements, stereochemistry of targeting by receptors, 133-139
Host-cell factor. See HCF HPRT gene, 316 HPV (human papillomavirus) type
16 E6/E7 and gene amplification, 648, 651- 652
HS2, HS3, and HS4 and LCR function, 3, 7-10
hsp26 and hsp70. See Heat shock genes
HSV (herpes simplex virus) VP16. See VP16
HTH. See Helix-turn-helix motif HU protein
in phage Mu transposition, 515- 517
transcription and replication coupling in ~., 390, 395- 396, 399-400
Human chromosomes. See Chromosome
Human excision nuclease, 605-615 Human genome mapping. See
Mapping Human immunodeficiency virus.
See HIV Human mismatch repair, 597-602 Human papillomavirus. See HPV
type 16 E6/E7 and gene amplification
Human RAD51 gene, 573-575 Human telomerase, 722 hus mutants, 639 Hybridization. See Alu-PCR
hybridization; CISS hybridization; Compara- tive genomic hybridiza- tion; FISH
Hydration in compaction of double
helix, 274 Hydration of proteins in solution,
NMR and X-ray diffrac- tion studies, 149-156
Hydroxyl radical cleavage pat- terns of nucleosomal DNA, 226-232
Hypersensitive regions. See DNase I sensitivity of chromatin
Hypervariable regions of trypanosome ESAGs, 110-111
I
ICD compartment. See Inter- chromosome domain compartment
ICP25. See VP16 IE promoter. See Immediate early
promoter of HSV IFN-~. See Interferon-~ gene Igf2 (insulin-like growth factor 2)
and receptor genes, 831 Igf2-H19 domain, differential
replication timing and allele-specific expres- sion, 307-312
methylation and imprinting, 282-283, 287, 293-294, 297-298, 301-303, 309- 312
Immediate early (IE) promoter of HSV, VP16 and Oct-1 in activation, 167-169, 176
Immune system. See also TCR and antigenic variation in
trypanosomes, 106, 110 Immunoglobulin K enhancer, 346 Immunoglobulin ~ enhancer, 97-
102 Immunolocalization of Sir3, Sir4,
and RAP1, 735-737, 741-744
Imprinting, 830-831 and DNA methylation, 282-283,
287-294, 297-304, 309- 312, 634
and fragile X syndrome, 634 and mating-type interconversion
in S. pombe, 457-464 and replication timing, 307-308,
310-311,634 Y chromosome and position-
effect variegation, 593- 594
INCENPs (inner centromere proteins)
as chromosome passenger proteins, 697-705
in mitosis, 680 Incision assay for excision repair,
606 Incision mechanism and DNA
repair, 626-628
SUBJECT INDEX 849
Initiation of transcription. See Preinitiation complex; RNA polymerase; Tran- scription
Initiator protein and initiation of replication. See Replica- tion of DNA
Insulator elements, 3-5, 22, 32, 46-47, 823. See also Fab- 7; Mcp; scs and scs t
Insulin gene and imprinted ex~ pression patterns, 307- 308
Insulin-like growth factor gene. See Ig['2 and receptor genes
Integration of DNA. See Retroviral DNA integration; Transposition
Interchromatin granule clusters and splicing, 785-786, 799-804, 813-814
Interchromosome domain (ICD) compartment, 778, 782, 786-788
Interfacial cavity, hydrated, 156 Interference
chiasma, 543-550 chromatid, 543
Interferon-~ gene (IFN-~), virus- induced enhancer com- plex and expression, 73- 80, 834
Interferon regulatory factor 1 (IRF-1), 77
Integration of DNA. See Retroviral DNA integration; Transposition
Interphase chromatin, 247-248 as random polymer, 771-772,
774 Interphase chromosome
functional organization of nucleus, 807-817
mapping and cytogenetic analy- sis with FISH, 771-774
territorial organization, 778 Inversions. See also Genomic se-
quencing FISH for cytogenetic analysis,
772-773 Gin inversion system of phage
Mu, 505-512 Invertebrates and DNA methyla-
tion, 281, 283 Inverted repeats. See Repeats Ionic strength
and processivity of telomerase, 713-716
and replication specificity, 391- 393, 400
IRF-1. See Interferon regulatory factor 1
I-Sce I sites, insertion of sites and physical mapping strategy, 358, 360
I silencers, 444. See also H M loci and repression
J
JB antigen, 699. See also IN- CENPs
J (joining) gene segment. See TCR Joining of DNA. See DNA ligases;
PARP. See also Repair of DNA
Joining (J) gene segment. See TCR
K
KEX2 ARS, 426-427. See also ARS Kinase activity
ofcdc2, 193, 638, 640 of CKII, 619, 621 of MPF, 193-195 of TFIIH, 187, 191-193, 195
Kinesins. See Mechanochemical motors
Kinetochore, 697. See also Centromere
CBF3 subunits in S. cerevisiae structure, 669-675
and chromosome passenger proteins, 699, 704
fibrous corona, 675 and FISH effect on nuclear to-
pography, 781-782 in S. pombe, 687
Kinetoplastida. See Trypanosomes "Kissing" interactions
in antisense RNA pairing, 554- 556
in pairing of homologous chromosomes, 554-557, 562
Klenow fragment of DNA polymerase I, crystal structure and mechan- ism, 495-503
K repeat in S. pombe centromere, 687-694
L
L1 fingerprinting for YAC contig map, 377-382
lac repressor, 824 retroviral DNA integration
targets, 533, 537-538 lacUV5 promoter and DNA bend-
ing in transcription in- itiation, 118-122
lacZ. See also ~-Galactosidase expression and enhancer trap-
ping, 590, 795-796 hsp26-lacZ fusion gene, 84
Lagging product site, 716-717 ~.. See Bacteriophage k Lamins A and C, 743-744
Lampbrush chromosomes, 45 loops and splicing, snRNPs,
747-749, 752 Large T antigen. See T antigen LBE. See Locus border element LCR (locus control region), globin,
97. See also Locus con- trol function
developmental stages and com- petition among genes for interaction, 10-12
HS2, HS3, and HS4, 7-10 in thalassemias, 7 and transcription control, 1-3, 5,
7, 32-33, 822-823 LEF-1. See Lymphoid enhancer
factor-1 Leptotene chromosomes, pairing.
See Chromosome, pair- ing of homologous
Leucine repeat. See Zipper proteins
LexA -controlled proteins. See SOS
response and function of SNF/SWI
proteins, 257-258 LexA-GAL4 fusion protein, 258,
437 LFS. See Li-Fraumeni syndrome Li-Fraumeni syndrome (LFS), 650,
661-662 LIG1, 621-622 Ligand-modulated transcription
factors. See Estrogen receptor; Glucocorticoid receptor; Nuclear non- steroidal receptors; Steroid receptor
Ligases. See DNA ligases; T4 ligase-mediated DNA cyclization
Li l ium and pairing of homologous chromosomes, 560, 563- 564
LIM15, 573-574 Linkage equilibrium at TCR locl,
342-343 Linkage map distance and
chiasma interference, 543-550
Linker histones. See H1; H5; Histones
Loci of genes, DNase sensitivity of chromatin, 37-39
Locus border element (LBE), 7 Locus control function, chicken
lysozyme gene, 37, 40- 42. See also LCR
Locus control region. See LCR Loops, DNA, 8, 45, 784, 786-787
and enhancer function, 823 in globin gene expression, 9-11 heterochromatin, 755-756, 758 HLH and b/HLH/Z transcription
factors, 123, 126-128
850 SUBJECT INDEX
Loops, DNA (continued) and HMG I(Y) role in IFN-~
gene expression, 79 lac repressor-induced, and
retroviral DNA integra- tion targets, 537-538
loop base and SARs, 755, 758- 759
loop body, detection, 758-759 and loop/scaffold model of
chromosomes, 755-758 and RNA splicing/processing,
747-749, 752 Loops, RNA, interaction of
homologous, 555 LTR. See MMTV LTR promoter Lymphoid enhancer factor-1 (LEF-
1), 78 Lysozyme gene
A element as insulator, 3, 823 chromatin domains as
regulatory units for tran- scription, 37-43
M
Macromolecules in solution, NMR and X-ray diffraction studies, 149-156
Macronuclear division in Tetrahymena, 708-711, 715
Macrophages, lysozyme gene and transcription regulation, 37-41
Maintenance methylation, 323- 324, 328
Maize telomere-length regulation, 720
MAP 2C, 702 Mapping
genetic and chiasma interference,
543-550 of protein/protein interaction
domains during Gin/FIS- mediated recombination, 505-511
yeast chromosomes, 363-364 physical, 349, 354, 544
Alu-PCR hybridization, YAC to YAC, 378-382
C. elegans genome, 367-368 chromatin structure, 84-85 chromosomal origins
2-D gel analysis of replica- tion intermediates, 415- 418, 425-426, 428-433, 436, 446-449, 467-472, 476-478, 490-491
3-D gel analysis in DNA puffs, 491
using radiolabeled nascent DNA, 476-478
contigs and cosmid finger-
printing, 349-351, 359, 367-368
DNA sequence copy number in, 646
FISH, 377-379, 382, 767-774 human genome, 377-382 L1 and THE fingerprinting of
YACs, 377-382 lysozyme locus control func-
tion, 40-41 nested chromosomal frag-
mentation and I-Sce I, 358, 360
resolution -completeness criterion,
349-355 with FISH in metaphase and
interphase chromosomes, 768-774
restriction, 351-352 STS-content, 349, 352-354,
368, 378-382 YACs, YAC contigs, and
MegaYACs, 368, 377- 382
yeast genome, 358, 360, 363- 364, 416
Marker overlap and ordering. See Mapping
MARs (nuclear matrix attachment regions), 25-29, 31-32. See also Scaffold, -associated regions
in generation of DNase-I- hypersensitive sites, 97- 102
lysozyme locus, 38, 42 MATal protein, 159, 161, 165 MATa2 homeodomain, structure
and DNA-binding specificity, 159-165
Mating-type interconversion and imprinting in S. pombe,
457-464 S. cerewsme, 443, 462-463
Mating-type-specific gene expres- sion. See a2 repressor; HM loci and repression
Max, X-ray crystal structure of b/HLH/Z form, 123, 126- 128
MCB (MulI cell-cycle box), 571, 638-639
MCBF. See DSC1 mcl (mitotic conditional lethals),
679 MCM1 protein, 159, 162, 165 Mcp, 51-52 m5C. See 5-Methylcytosine Mechanochemical motors, 683,
697. See also INCENPs; mukB and chromosome segregation
and NTP-binding motif, 681 MeCP1. See Methyl-CpG binding
protein
MegaYACs. See YACs Meiosis
-II-type separation in meiosis I in S. pombe, 690-692
and premeiosis, unstable inter- actions in pairing of homologous chromosomes, 553-564
Meiotic recombination. See Recom- bination
Metaphase to anaphase transition. See Chromosome, segregation
Metaphase chromosomes banding and SARs, 755-764 FISH and chromosome map
resolution, 768-774 Methotrexate (Mtx), 650, 657, 662,
664 Methylase. See dam methylase Methylation of deoxyadenosine.
See dam methylase Methylation of DNA, 281,319,
331,450, 539. See also Methyltransferases
ancestral protective function, 283
copy-number- and position- dependent in Neurospora, 325-328
de novo, 283, 324-325, 328 and embryonic development,
300, 303-304 and fragile X syndrome, 634 in imprinting, 282-283,288-
294, 297-304, 309-312, 634, 831
maintenance, 323-324, 328 non-CpG in Neurospora, 323 and replication control and
timing, 384-385, 634 and RIP mutation, 283,327-329 signal in Neurospora ~-~l region,
323-329 in transcription repression and
silencing, 281-284, 289, 293, 300-301,634
Methyl-CpG binding protein (MeCP1), 281-282
5-Methylcytosine (m5C), distribu- tion in genome, 281,283. See also Methylation of DNA; Methyltrans- ferases
Methyl-directed mismatch repair. See Mismatch repair
Methyl green (MG) quenching, staining loop bodies with YOYO-1, 758-763
Methyl-methane sulfonate (MMS) damage to DNA, repair. See RAD proteins, Rad51
N-Methyl-N i -nitro-N- nitrosoguanidine. See MNNG
Methyltransferases (MTases), 288,
SUBJECT INDEX 851
297, 331. See also Methylation of DNA
HhaI crystal structure, 331-337 homologous recombination of
gene in study of methylation, imprinting, and mammalian devel- opment, 297-304
mfd gene product, 613, 630 MG. See Methyl green quenching MIC2 and X inactivation, 316-317 Microinjection
for studying pre-mRNA splicing, 8O2
of telomerase RNA gene, 708- 7O9
of YAC DNA in generating transgenic mice, 55-56, 58
Microsatellite STSs. See STS- content mapping, human genome
Microtubule, 669, 673-675, 677, 788-789, 794. See also Centromere; Kinetochore
assembly inhibitor. See Nocodazole
-associated proteins of nerve cells, 702
-binding activity of centromeres, 674, 681-683
and chromosome passenger proteins, 697-705
Mimosine, replication inhibitor, 468-473
rnin CDE system and cell division, 386
Minichromosomes BPV-1,408-409 Dp1187 and Dp400, genomic in-
stability in position- effect variegation, 585- 590
S. cerevisiae and centromere function, 682-
683 and chromatin-mediated tran-
scription repression, 237-244
and S. pombe centromere func- tion, 687-688, 690-694
TRPIARS1 and SV40, retroviral DNA integration target, 534-536
Minicircle DNA DNA bending and retroviral
DNA integration, 538 topoisomers, RNA polymerase
binding and DNA bend- ing, 117-122
Mismatch repair, 597-602 Mitomycin C, 612 Mitosis. See Centromere;
Chromosome, condensa- tion; Chromosome, segregation; INCENPs;
Sister chromatids Mitosis promoting factor. See MPF Mitotic inhibitor. See Nocodazole Mitotic spindle and spindle pole
bodies, 677. See also Centromere; Kinetochore
association with CBF2p, 670, 675
centromeric repeat and spindle attachment, 690-692, 694
and chromosome passenger proteins, 697-705
spindle integrity and DSC1, 680 MLV (murine leukemia virus), in-
tegration target and in- tegrase, 534-538
MMS (methyl-methane sulfonate) damage to DNA, repair. See RAD proteins, Radhl
MMTV LTR (mouse mammary tumor virus long termi- nal repeat) promoter
activation and nucleosome orga- nization, 63-70, 825
and gene remodeling, 83, 88 MNNG (N-methyl-N ~ -nitro-N-
nitrosoguanidine), 600- 601
Motor proteins. See INCENPs; Mechanochemical motors; mukB and chromosome segregation
Mouse chromosome 7. See Chromosome
Mouse mammary tumor virus long terminal repeat. See MMTV LTR promoter
Mouse RAD51 gene, 573-575 MPF (mitosis promoting factor),
role in RNA polymerase II phosphorylation, 193- 195
mRNA transcription and process- ing. See Splicing; Tran- scription
mRNA-type promoter, VP16 and Oct-2 activation, 167- 169
MSA-36, 699. See also INCENPs MTases. See Methyltransferases Mtx. See Methotrexate Mu bacteriophage. See Phage Mu mukB and chromosome segrega-
tion, 385 MulI cell-cycle box. See MCB Murine leukemia virus. See MLV Mutations
in cis-regulatory units of bithorax complex, 51
-driven model of tumorigenesis, 655
missense, for DNA ligase I, 621- 622
point CpG to TpG transitions, 622
RIP, and DNA methylation, 283, 327-329
for recombination. See RAD proteins
suppressor, for FIS-independent Gin-mediated recom- bination, 507-511
temperature-sensitive. See also cdc mutations, genes, and proteins
and ARS function at HMR-E, 437, 449-450, 452
in study of macronuclear divi- sion and telomeric se- quences, 709-711, 715
in study of ORC, 437-439 in study of sister chromatid
pairing and chromosome condensation in mitosis, 679-680
MutH and strand breaks, 597-598 c-myc, DNA domains containing
single-copy genes, 29-32 Myc oncoproteins, 126 Myelomonocytic lineage, ]ysozyme
gene and transcription regulation, 37, 39-40
MyoD, 821, 826, 833
N
NAT1/ARD1 genes, 733 NDCIO/CBF2, 669, 674 Nematode. See Caenorhabditis
elegans Neoplasia
and loss of genomic integrity. See Gene amplification
and telomere length, 721-722 Nested yeast chromosomal frag-
mentation. See Mapping Neurospora crassa, 544, 553,829
ancestral function of DNA methylation, 283
DNA methylation signal in ~-~1 region, 323-329
RIP mutation, 283, 327-329 Nevirapine cocrystallized with
reverse transcriptase, 495, 499-500
NF1/CTF, 64, 66-70 NF-E2 and globin gene expression,
8-9 NF-~B and virus induction of IFN-
gene, 74-79, 834 Nicked DNA. See DNA nifS gene, 359 NMR (nuclear magnetic
resonance) spectroscopy studies
DNA-binding domains of Tram- track and hormone receptor, 134, 141-146
protein hydration, 149-156 Nocodazole, 483, 678-680
852 SUBJECT INDEX
NOEs (nuclear Overhauser ef- fects), measurements for protein hydration, 150- 154
Nonnucleoside inhibitor binding to reverse transcriptase, 499-500
NTP (nucleoside triphosphate) -binding motif of mechanochemi-
cal motors, 681 -binding sites and helicase motif,
259-262 Nuclear envelope (nuclear mem-
brane), 697, 788-789 and chromatin interaction, 248,
794 and gene-gating model of export,
794-796 and heterochromatin repression,
254 and licensing factor model of
coupling cell cycle to replication, 639
telomere attachment, 557 and telomere positioning by
SIR3 and SIR4, 735-737, 741-744, 830
Nuclear hormone receptors. See Estrogen receptor; Glucocorticoid receptor; Steroid receptor
Nuclear magnetic resonance. See NMR spectroscopy studies
Nuclear matrix, 789, 815. See also MARs; Scaffold, -associated regions
Nuclear membrane. See Nuclear envelope
Nuclear nonsteroidal receptors, stereochemistry of inter- actions, 133-134, 136
Nuclear Overhauser effects. See NOEs
Nuclear RNA transcripts. See Nucleus; RNA, trans- cripts; snRNA and snRNPs
Nuclear scaffold. See Scaffold Nuclear skeleton. See Nuclear
matrix Nuclease~ regions.
See DNase I sensitivity of chromatin
Nucleolar bodies. See Prenucleolar bodies
Nucleolus, 807, 813, 816. See also snoRNPs
organizers, 591-592 and RNA synthesis, 747
Nucleoplasmin, 219, 221 Nucleoprotein filaments (helical)
formation by RecA and Radhl proteins, 567, 569
Nucleoside (modified) in silencing ofVSG gene, 108-109
Nucleoside triphosphate. See NTP Nucleosomal templates, 207-208 Nucleosomes, 273. See also
Chromatin; Histones A, 63, 70 array, 1, 45, 63, 83
discontinuities. See DNase I sensitivity of chromatin, hypersensitivity regions
effect of centromeric repeats, 692
in remodeled vs. preset genes, 83, 88
hsp26 as preset gene, 83-95 B of MMTV LTR, 63-70 construction and disruption of,
225-232 facilitated binding of GAL4 to
cores, 216-217, 221-222 footprinting cores, 65 helical repeats and discontinuity
of core DNA, 226, 228, 231-232
in higher-order chromatin struc- ture, 15, 18-22, 45, 83- 84
and hormone receptors, 63-64, 66, 69, 94
and hsp26 gene insertion into heterochromatin, 92-95
-like structure. See O-some positioning and modification in
transcription, 1, 4-5, 32, 63, 222, 234, 253, 533- 534, 824
effect in regulating gene ex- pression, 88, 92, 94-95, 237-244
and factor access. See Tram scription factors
mechanism, 65-66 "positioning" proteins, 94 in replication, 403, 408-409 and retroviral DNA integration
target, 533-540 role in transcription activa-
tion/repression, 83, 213 222, 824-825
structure comparison with histone oc-
tamer, rods of densities, 277-278
of core particle and histone location assignments, 265-271
in telomeres, 251 Nucleotide excision repair. See Ex-
cision and gap repair Nucleotide misincorporation,
reverse transcriptase vs. Klenew fragment, 495, 502-503
Nucleotide pool perturbation. See Antimetabolites
Nucleus. See also Nuclear en- velope; Nucleolus;
Pronucleus; snoRNPs; snRNA and snRNPs
compacting chromosomal DNA within. See Chromatin
electric forces on chromosome territories, 787-789
functional compartmentaliza- tion, 807-817, 835
and chromosome territories, 777-789
localizing RNA transcripts and splicing/processing, 747- 753, 784-787, 793-797, 799-804, 807, 810-817
organization and site-specific replication initiation in metazoan chromosomes, 475-484
topography and FISH analysis, 781-782, 789, 808-810
O
OBR (origin of bidirectional replication), 475-484. See also Replication of DNA, origin
Oct-1 and Oct-2 homeodomain proteins, DNA-binding specificity and differen- tial transcriptional regulation, 167-176, 826
Octamers. See Histones Oligonucleosomes in [3-globin
domain, solubility and structural stability, 15, 18-22
Oncogenic viruses in study of gene amplification, 648, 651- 652
Oocytes. See Xenopus Open complex of transcription in-
itiation and DNA bending, 116-118, 121 and TFIIH DNA helicase ac-
tivity, 193 Operators
a2, chromatin near, 237-244 MATa2, 162
O protein in k replication, 389, 391, 398, 4OO
ORC (origin recognition complex), yeast initiator protein, 437-441,830
Sciara equivalent, 492 orf-26, 526 ori. See Replication of DNA, origin Origin recognition complex. See
ORC Origin of replication. See Replica-
tion of DNA Orphan genes in yeast, 359, 361 O-some, 389, 398-399 Ovalbumin probe, DNase
sensitivity of ~-globin domain, 16-22
SUBJECT INDEX 853
P
p34 cdc2 kinase. See cdc mutations, genes, and proteins
p53 GAL4-p53(1-73) and DNA
replication, 410, 412 tumor suppressor gene, role in
gene amplification and cell cycle checkpoint con- trol, 645, 649-651,658- 664, 832
Packaging chromatin. See Chromatin
Packaging chromosomes for mitosis. See Chromo- some, condensation
Paired ends of helices motif of histone octamer, 277
Pairing, 577. See also Recombina- tion; Repair of DNA
antisense RNA, 554-556 of homologous chromosomes, un-
stable interactions in, 553-564
of sister chromatids. See Sister chrematids
Pairing-sensitive elements and cis- regulatory units of bithorax complex, 48-53
Pairing-sensitive repression of white minigene, 52-53
Pair-rule transcript localization. See Drosophila
PALA (N-[phosphonoacetyl]-L- aspartate), CAD gene amplification and arrest of cell cycle, 647-652, 656-664
Papillomavirus. See BPV; HPV type 16 E6/E7 and gene amplification
Parallel 13 bridge of histone oc- tamer, 277
Parental genotype and variega- tion, 593
Parental imprinting. See Imprint- ing
PARP (poly[ADP-ribose] polymerase), role in DNA joining, 619, 622- 623
PCNA (proliferating cell nuclear antigen), 606, 615, 628- 629, 631
PCR (polymerase chain reaction). See also Alu-PCR hybridization
-based assay for retroviral DNA integration, 533-536
P element and enhancer trapping, 586, 795 and position-effect variegation,
593
insertion in Dp1187 mini- chromosome, 586
and P-transposase-induced deletions, brown gene, 578-583
white gene insertion in heterochromatin, 84, 86, 93-95
Perichromatin fibrils and coor- dination of transcription and splicing, 785-786, 799-804, 813
PEV (position-effect variegation). See Heterochromatin
PGK1 and X inactivation, 316-317 Phage Mu
inversion system. See Gin/FIS- mediated site-specific recombination
transposition and target site preference at DNA strand transfer, 515-522
Phenotype, variegating. See Heterochromatin
P H 0 5 promoter, 83, 88 N-(Phosphonoacetyl)-L-aspartate.
See PALA Phosphorylation
in control of DNA replication and mitotic checkpoint, 638, 640
/dephosphorylation ofDNA ligases, 619-621 of DNA topoisomerase II, 621
of RNA polymerase II carboxy- terminal domain, 187, 190-197
Photoproduct repair, 613, 626 Physical mapping. See Mapping PIC. See Preinitiation complex Point mutations. See Mutations pol I, II, III. See RNA polymerase POLA and X inactivation, 316-318 Poly(ADP-ribose) polymerase. See
PARP Poly(A) RNA and pre-mRNA
metabolism, 799, 813-817
Polycomb group genes and proteins, 49-50, 52-53, 247,788, 823, 831
Polymerase chain reaction. See PCR
Polymerases. See DNA polymerases; PARP; RNA polymerase
Polymorphic STS mapping. See STS-content mapping, human genome
Polynucleosome array. See Nucleosomes
Polyomavirus large T antigen, 404-405, 482-483
Polytene chromosomes, 45, 487, 491, 544
Position-dependent methylation.
See Methylation of DNA Position effects on gene expres-
sion. See Gene expres- sion; Telomere
Position-effect variegation (PEV). See Heterochromatin
Positioning of nucleosomes. See Nucleosomes
Posttranslational regulation of DNA ligase I, 621
Potassium glutamate and replica- tion specificity, 391-393, 400
POU homeodomain proteins Oct-1 and Oct-2, 167-176
P protein in ~ replication, 389, 391,398, 400
Prader-Willi/Angelman syndromes, 308, 311
PRDs. See Domains, positive regulatory
Preinitiation complex (PIC) assembly, 123, 125, 187-188
effect of transcriptional ac- tivators, 199-202
and nucleosome core/H1 inhibi- tion, 222
and replication, 409, 638 BPV-1,404, 412 ~, 389, 393
and RNA polymerase phosphorylation, 187, 190-197
stable association with polymerase, GTF roles, 187-190
Premeiotic cells, unstable interac- tions in pairing of homologous chromosomes, 553-564
Pre-mRNA processing and splic- ing. See Splicing
Prenucleolar bodies, snoRNAs in, 750-753
Pre-rRNA processing and snur- posomes, 747, 749-750, 752-753
Primase in ~ replication. See Bac-
teriophage :polymerase c~ and replication in-
itiation, 412, 637 Processing of transcripts. See Pre-
rRNA processing and snurposomes; Splicing
Processivity. See also RNA polymerase
ofE. coli RNA polymerase, 716 of telomerase, 711-717
Progesterone receptor, transcrip- tional activation and regulation, 68
Prokaryotic DNA invertases, 505. See also Inversions
Proliferating cell nuclear antigen. See PCNA
854 SUBJECT INDEX
Promoter. See also Gene expres- sion; Transcription
activity and nucleosome-free regions, 83
~A-globin, 1, 17-18 -binding factors in antirepres-
sion, 205-212 core element in transcription
regulation, 123, 187. See also TATA box
cryptic and function of DNA methyla-
tion, 282, 284 and effect of LCR on chromatin
structure, 1-3, 5 enhancer core and genera-
tion of DNase-I- hypersensitivity sites, 97-102
GALl vs. CYC1 activation by SNF/SWI, 258
H19 gene and imprinting, 289- 291,293
hormone-receptor binding in ac- tivation, 63-64, 66, 68- 70
HSV IE, VP16 and Oct-1 activa- tion, 167-169, 176
IFN-~, 73-80 Igf2 gene, 293 Kriippel. See GAGA factor lacUVh, DNA bending in tran-
scription initiation, 118- 122
MMTV LTR, 63-70, 825 mRNA-type, Oct-2 and VP16 ac-
tivation, 167-169 proximal elements in transcrip-
tion regulation, 123. See also Max
remodeling in activation, 83, 88 repression of. See Transcription,
repression and silencing -selective transcription factors,
179-184 o model of recognition, 179, 188 snRNA, Oct-1 activation, 167-
168 strength and DNA methylation,
281-282 SV40 early, 179 T7, ~ enhancer-mediated acces-
sibility and chromosomal position-independence, 97-102
TATA-containing, assembly of preinitiation complex on. See Preinitiation com- plex
TATA-deficient, role of TBP, 125, 181
and topological organization of domains, 33
Pronucleus microinjection ofYAC DNA into,
55-56, 58
snRNAs and snoRNAs in, 750- 753
Protein/DNA complexes and inter- actions, 515. See also cL2 repressor; Catabolite ac- tivator protein; DNA, bending; Domains; En- hancer; GAGA factor; GAL4; HhaI crystal structure; Histones; Homeodomain proteins; lac repressor; LexA; ORC; PARP; Rapl/RAP1; RecA; Recombination; RNA polymerase; RPA; RuvABC proteins; Tran- scription factors; Zinc fingers and zinc- stabilized motifs
involvement of hydration water in recognition, 155-156
relation between DNA bending and binding strength in, 115-122
structural studies. See X-ray crystal structure
Protein hydration in solution, NMR and X-ray diffrac- tion studies, 149-156
Protein-protein interactions, map- ping domains involved in. See Gin/FIS-mediated site-specific recombina- tion
Protein structure, 826-827 determination of. See NMR spec-
troscopy studies; X-ray crystal structure
of hydrated molecules in physiological milieus, 149, 154-155
internal mobility, 149, 153 on surface, and molecular recog-
nition, 149, 156 Protein supercoil of histone oc-
tamer, 276-279 Provirus. See Retroviral DNA in-
tegration Pseudoautosomal region and
boundary, 316-317 Pseudogenes and genomic se-
quencing, 341-342 Puffs, DNA amplification and
transcription in, 487- 493
Pyridoxyl 5 ' phosphate cross- linking to reverse trans- criptase and Klenow fragment, 497-498
Pyrimidine dimers and DNA repair. See Excision and gap repair
Pyrimidine precursor synthesis in- hibition by PALA, 647- 651
Pyrophosphate inhibition of telomerase, 712-713
Q
Q-bands, 756-764 Quinacrine staining, 756
R
RAD proteins in excision repair, 611-613, 625,
627 RAD9, cell cycle checkpoint con-
trol, 651,657-658, 731, 832
Radhl, homology to RecA, domains, and DNA recombination/repair function, 567-575
rad52, 720 Rad52, strand-transfer activity
and DNA repair, 567- 569
Rad52- host strain for MegaYACS, 378
Radiation-sensitive mutants. See RAD proteins
Rapl/RAP1 (repressor activator protein 1)
and chromosome stability, 734, 744
immunolocalization, 735-737, 743-744
for replication origin function, 448, 452
in silencing, 250, 254, 444, 449, 733, 743-744
and telomere length, 720, 733- 734, 737, 739, 744
R-bands, 756-764 Rb-dependent cell cycle arrest, 664 RCC1 mutations, 642 rDNA, 591-592 rDNA ARS. See ARS RecA
-like recombination/repair proteins in eukaryotes, 567-575
-mediated recombination/repair, 525, 528, 567
Receptors. See also Estrogen receptor; Glucocorticoid receptor; Igf2 and recep- tor genes; Progesterone receptor; Retinoid recep- tors; Steroid receptor; TCR; Thyroid hormone receptor; Vitamin D 3 receptor
for uptake in trypanosomes, antigenic variation, 110- 111
RecG, 529-530
SUBJECT INDEX 855
Recombination. See also Homologous recombina- tion; Mating-type inter- conversion
branch migration and Holliday junction resolution by Ruv proteins, 525-530
chiasma interference in Drosophila, 543-550
crossovers and homologous pair- ing of chromosomes, 556
fidelity. See Mismatch repair frequency
additivity, 543 following damage, 525
Gin/FIS-mediated site-specific inversion, 505-512
recA, function and homology. See RecA
retroviral DNA integration, 521, 533-534
nucleosomal DNA as target, 533-540
and SOS response, 525-526, 528 telomere-telomere in yeast
telomere replication, 725, 731
transposition of phage Mu, target-site pref-
erence at DNA strand transfer, 515-522
of Tyl and Ty3, integration target, 539-540
Recombination nodules and crossing-over, 548
Repair of DNA, 525, 529, 625. See also DNA ligases; Mating-type interconver- sion; PARP; RecA; Recombination
excision and gap repair, 578, 581,598, 625-631
excinuclease and Xeroderma pigmentosum, 605-615
mismatch repair, 597-602 postreplication gap repair, 528-
530 and SOS response, 525-526, 528 species-specificity of Rad51 and
Rad52 in, 574-575 transcription-dependent, 612-
613, 615, 629-630 Repair synthesis assay, 606 Repeat-induced point (RIP) muta-
tion and DNA methyla- tion, 283, 327-329
Repeat, long terminal. See MMTV LTR promoter
Repeat polymorphisms in TCR loci, 342-343
Repeats, tandem and inverted att sites, 533-534 in C-bands, 756, 758 and function of DNA elimina-
tion, 591-592 gtx, 505-506
in S. pombe centromere, 687- 694
in telomeres, 707, 711, 719-720, 725
Replication bands, 311 Replication of DNA. See also
Abfl/ABF1; ARS; DNA polymerases; Preinitia- tion complex; Rapl/RAP1
antirepression and E2, 408-409, 411
BPV as model, problems, 482- 484
cell membrane in control, 384- 385
and chromatin assembly, 233, 408-409, 412, 453, 478- 482,484
chromosomal replication inter- mediates
analysis of origin and direction of fork movement. See Mapping
2-D gel analysis of direction of fork movement and timing of telomere replication, 727-728
and chromosome breakage, 656- 657
circle-to-circle in K, 389, 392, 399 of ColE1, antisense RNA pairing
in, 555-556 control. See also Replication of
DNA, timing coordinating with cell cycle,
384-386, 487, 637-642, 832
methylation of DNA in, 384- 385, 634
by protein phosphorylation, 638, 640
replicon model of regulation, 383-386, 435, 467
and dnaA protein, 384-385 ecdysone regulation and DNase-
I hypersensitivity in, 491-493
in heterochromatic regions, 250, 254
initiation, 384 and enhancer proteins in BPV-
1,404-412 in k in vitro, directionality and
effect of transcription, 389-400
selective inhibitor. See Mimosine
site-specific in Xenopus, role of nuclear organization, 478-484
in SV40, 637 initiator protein, 384, 467
in SV40. See T antigen in yeast, 436-441
nucleosomes and positioning in.
See Nucleosomes origin, 25, 32, 384, 405-406
of mammalian DHFR locus, 467-472
OBR in metazoan chromosomes, 475-484
oriC in E. coli, 384-386 orig., 389 in S. coprophila DNA puff,
488, 490-493 trans-acting factor in regula-
tion, 491 yeast, 386
activity of ARS elements, 415-422, 425-433, 435- 436
ORC as initiator protein at, 437-441,830
position effect, 421-422, 426-427
transcriptional silencer as, 443-454, 830
and pairing of sister chromatids, 677, 679
replication fork barriers/pause sites, 421,432
replication fork mechanism, 475
replication/repair proteins. See PCNA; RPA
role in establishing repressed state, 443-454
rolling-circle in K, 389, 392, 399 semiconservative, 458, 480, 627-
629 specificity in vitro and ionic
strength, 391-393, 400 T4, 398 of telomeres, 719, 725-731 termination in yeast, 431-433 timing
and allele-specific expression, 307-308, 310-311, 634, 831
ARS1, ARS305, ARS501, and KEX2 ARS, 426-427
and chromosome bands, 756 delayed, fragile X syndrome
and thalassemia, 633- 634
and telomeres, 427, 725-731 Replicative transposition of phage
Mu. See Phage Mu Replicon model of replication. See
Replication of DNA Repression of transcription. See
Insulator elements; Transcription, repres- sion and silencing
Residence times of water molecules in hydration sites, 151-152, 155-156
Resolution of Holliday junctions. See Holliday junctions
Resolution of maps. See Mapping Resolvases, 506, 508, 529-530
856 SUBJECT INDEX
Restriction enzymes hormone-dependent access to
nucleosome B DNA of MMTV LTR, 66
in mapping. See also Mapping Alu-PCR hybridization, YAC
to YAC, 378-382 chromatin structure, 84-85 nested chromosomal frag-
mentation and I-Sce I, 358, 360
S. cerevisiae chromosomes, resolution-completeness profile, 351-352
methylation-sensitive, 289, 323 HhaI crystal structure, 331-
337 Retinoid receptors, 133-134, 136 Retrotransposons. See
Transposons and retrotransposons
Retroviral DNA integration, 521, 533-534
nucleosomal DNA as target, 533-540
Reverse transcriptase HIV, crystal structure and me-
chanism, 495-503 telomerase as specialized, 708
RFC, 629, 631 Ribonucleoproteins. See sneRNPs;
snRNA and snRNPs Rifl (RAPl-interacting factor 1),
720, 744 RIP. See Repeat-induced point
mutation and DNA methylation
RNA. See also Poly(A) RNA and pre-mRNA metabolism; rRNA; snRNA and snRNPs; tRNA genes
antisense, pairing, 554-556 processing. See pre-rRNA pro-
cessing and snur- posomes; Splicing
synthesis inhibition and cell cycle arrest. See Antimetabolites
telomerase, 707-717, 719-720 transcripts
localization in nucleus, tran- script domains, and ex- port. See Nucleus
"track"- or "dot"-like accumula- tion, 784-785, 796, 810- 813, 815
RNA polymerase, 32. See also Transcription
c~-amanitin sensitivity, 800 I in transcription initiation, 123,
181-182 II
binding and DNA bending re- lationships, 115-122
at perichromatin fibrils, 785, 8O0-804
phosphorylation role in tran- scription initia- tion/elongation cycling, 187-197
promoter- and enhancer- binding factors in regulating, 205-212
o factors and promoter specificity, 188
and transcription initiation, 123, 199, 629
and nucleosomes, 83, 241- 242
TBP and TAF role, 179-184 III, 123, 181-182, 241,243 E. colt, 716
and directionality of ~. replica- tion, 395-399
and T4 replication system, 398 T7, interaction with DNA, 97-
102 in transcription, effect of
chromatin structure, 4- 5, 63, 825. See also Chromatin; Transcrip- tion
RNase H, 802 and k replication, 396, 399-400 domain of reverse transcriptase,
495, 499-501 Rods of densities of nucleosome
and octamer structures, 278
Rolling-circle replication. See Replication of DNA
RPA, 405, 411,642,825 in BPV-1 replication, 410-412 in excision repair, 627-628, 631
rRNA genes and pseudogenes, 323, 813
domains and MARs, 26-29 factor access in nucleosome
containing, 225-234 processing, 807. See also pre-
rRNA processing and snurposomes
transcription and SL1, 181-182 RuvABC proteins, branch migra-
tion and Hollidayjunc- tion resolution, 525-530
S
Saccharomyces cerevisiae. See Yeast
SARs. See Scaffold, -associated regions
SC1,755 SC-35 splicing factor, 800-801,
813-816 Scaffold. See also Loops
-associated regions (SARs), 79. See also MARs
and chromosome banding, 755-764
daunomycin selective stain, 758-764
HMG I(Y) binding, 79, 755, 763
and topoisomerase II, 755, 763 /loop model of chromosomes,
755-758 protein SC1,755
Schizosaccharomyces pombe. See Yeast
Seiara coprophila, DNA puff amplification, 487-493
scs and scs t, 3, 32, 45-48, 823. See also Insulator ele- ments
Segmentation genes, 48-53, 793- 794
Segregation of chromosomes. See Centromere; Chromosome; Kinetochore; Strand- segregation model
Selective pressures of histones, 278
Senescence and telemere length, 721
Sequence conservation. See Evolu- tion
Sequence-specific DNA recognition by transcription factors. See Transcription factors
Sequence-specificity of phage Mu transposition, 515-522
Sequence-tagged sites. See STS- content mapping
Sequencing. See Genomic sequenc- ing
o factors, 179, 188, 821-822, 833 Silencing of genes. See Transcrip-
tion, repression and silencing
Single-copy genes, detecting domains containing, 29- 31
Single-stranded DNA-binding protein. See RPA
Sir/SIR proteins in positioning and length of
yeast telomeres, 733-745 and silencing of yeast mating-
type loci, 249-255, 443- 445, 450-452, 733-734, 737-740, 743-744, 824, 829-830
Sister chromatids attachment in meiosis I and
centromere-specific repeats, 690-692, 694
disjunction and movement. See Chromosome, segrega- tion
pairing, 677-680 SL1, TBP and TAF role, 181-182 Small nuclear RNA and
riboproteins. See snRNA and snRNPs
SUBJECT INDEX 857
Small nucleolar riboproteins. See snoRNPs
Sm antigen, 785-786 SMC1 in mitotic chromosome
segregation, 680-681 SNF/SWI proteins in transcrip-
tional activation, 257- 262, 825
snoRNPs (small nucleolar riboproteins), 747, 749- 752
snRNA and snRNPs (small nuclear RNA and riboproteins)
imprinted gene, 287, 307-308, 311
snRNA promoter, Oct-1 activa- tion, 167-168
in splicing and processing of nuclear transcripts, 747- 753, 785-787, 799, 802, 804, 813-817
Snurposomes, RNA processing, 747-753. See also snRNA and snRNPs
Solenoidal structure of DNA, 1, 45, 63, 69, 83, 248
Somatic cell hybrids in obtaining YAC contig map of
human genome, 378-379 in study of gene amplification,
649 in study of X-linked gene expres-
sion, 315-321 Somatic cells, unstable interac-
tions in pairing of homologous chromosomes, 553-564
Somatic DNA instability. See Genome, stability
Somatic pairing, role in trans- inactivation and domi- nant variegation, 577
Sordaria and pairing of homologous chromosomes, 553, 558- 560
SOS response, recombina- tion/repair proteins in, 525-526, 528
Spl, 8, 74 in antirepression, 206-207, 209-
210 TBP and TAF role, 179-181, 183
Specialized chromatin structures in Drosophila. See scs and scs ~ in silencing yeast genes, 250-
254 S phase. See Cell cycle Sphere organelles, 749, 752 Spindle. See Mitotic spindle and
spindle pole bodies Splicing
nuclear recruiting mechanism and snRNPs in, 747-749, 752-753, 785-787, 799-
804, 813-815 nuclear RNA tracks as site, 810-
813 pattern alterations from dis-
rupted DNA methyltransferase gene, 299-300
and transcript domains, 799, 813-817
trans-splicing in trypanosome mRNA synthesis, 105- 106
Spodoptera HCF, 171-173 Sporulation, zygotic, 459 5S rRNA genes and pseudogenes.
See rRNA SSL2/RAD25, 611 STE6 gene, nucleosome position-
ing, 238-241 Steroid molting hormone. See Ec-
dysone Steroid receptor, transcriptional
activation and regula- tion, 63-64, 66, 69, 73, 133
stereochemistry of DNA interac- tion, 133-139
STH1 helicase-like domain, 259- 260
Strand breaks joining. SeeDNA ligases; PARP.
See also Repair of DNA MutH-introduced, 597-598
Strand exchange or transfer. See Recombination
Strand-segregation model, mating- type interconversion, 457-458, 460
Strand-specific mismatch repair. See Mismatch repair
Streptavidin/colloidal gold to visualize repair event, 626
STS (sequence-tagged site)- content mapping, 349, 354
human genome, 378-382 resolution-completeness profiles
in human Y chromosome, 352-353
for YAC-YAC linkage in C. elegans chromosome, 368
Supercoiled DNA. See DNA Supercoiled protein of histone oc-
tamer, 276-279 Suppressors
of FIS-independent phenotype for Gin-mediated recom- bination, 507-511
stage-specific for globin genes, 10
Surface elements of histone oc- tamer, 277
Surface hydration of proteins, 149-156
SV40
early promoter, 179 minichromosome and retroviral
DNA integration target, 534, 536, 540
replication origin, 482-483 replication and T antigen, 411-
412, 637, 638 T antigen and CAD gene
amplification, 648 SWI/swi, 638-639
DNA cleavage and mating-type interconversion, 458- 462, 464
in transcriptional activation, 257-262, 825
Switching genes. See SWI/swi Syn aptic/syn aptonemal complex
(SC) of Gin/FIS-mediated recombina-
tion, 505-506, 508, 511- 512
and homologous pairing, 553, 556, 561
of phage Mu transposition, 515- 516
Synthesis of DNA. See Replication of DNA; Telomere, and telomerase
T
T antigen, 404-405, 411-412, 482- 483, 637-638, 648
T4 ligase-mediated DNA cycliza- tion, 118-119
T4 replication system, 398 T7 promoter and RNA polymerase,
97-102 TAFs (TBP-associated factors),
123, 199, 202, 827-828 and coactivator activity of
TFIID, SL1, and TFIIIB, 181-184
Tandem repeats. See Repeats TATA box, 66, 87, 89, 93-94, 123,
222, 440, 824 -binding protein (TBP), 87-88,
123-124, 187-189, 199, 202. See also TAFs
phosphorylation-dependent in- teraction with RNA polymerase II, 190, 192, 195-197
in promoter-selective tran- scription initiation, 180- 184
X-ray crystallographic studies of TBP-2, 123-126
and positioned nucleosomes, 238, 240-241, 824
promoters containing, assembly of preinitiation complex on. See Preinitiation complex
promoters deficient in, TBP role, 125, 181
858 SUBJECT INDEX
z, 702 TBP. See TATA box, -binding
protein TBP-associated factors. See TAFs T-cell receptor. See TCR TCR (T-cell receptor)
-(z gene enhancer, 78 loci and genes, 622, 835
comparative large-scale DNA sequence analyses, 339- 347
evolution in mouse and hu- man, 343-346
polypeptide regions and gene segments, 339
trypsinogen gene family in se- quence, 346-347
TD-60, 699. See also INCENPs Telomere, 657, 683, 830. See also
Genomic sequencing "bouquet formation", 557, 741 and chromosome pairing via un-
stable interactions, 557- 558, 561
histone role in repression, 252 length, 720-722
RAP1 and sir3 and sir4 muta- tions effect, 733-734, 737-740, 744
and repression of VSG gene expression, 107-109
and macronuclear division, 708- 711, 715
mapping in C. elegans, 368 and replication origin activity
and timing of ARS ele- ments, 421-422, 427
replication in yeast, 725-731 repression and position effects in
yeast, 249-255, 421-422, 427, 725, 733, 743-744
SIR3 and SIR4 in perinuclear positioning, 735-737, 741-744
sub-telomeric DNA modification in repressing expression, 108-109
and telomerase, 707-717, 719- 720, 722, 725, 832
and trypanosome VSG gene ex- pression and silencing, 106-112
Temperature-sensitive mutants. See Mutations
Templates. See also Replication of DNA; Transcription
chromatin for BPV-1 replication, 408-409, 411-412
chromatin vs. histone-free for DNA transcription, 207- 209
function of telomerase RNA as, 707-711,716
nucleosomal, 207-208 specificity for ~. replication. See
Bacteriophage ~.
transcription factor interaction, 67-69
Tetrads and chiasma interference, 543-
550 frequency estimates, exchange
rates, and standard er- rors, 550-552
Tetrahymena telomeres length regulation, 720-721 and telomerase, 707-717, 719-
720, 725, 832 TF. See Transcription factors TFBP. See Transferrin-binding
protein and receptor Thalassemias, 7, 634 THE fingerprinting for YAC contig
map, 378-382 T-helper cells, 339 0-structure replication. See
Replication of DNA, circle-to-circle in ~.
Thymine dimer removal from DNA, 605, 626. See also Excinuclease in DNA repair
Thyroid hormone receptor, 133- 134, 136
T-killer cells, 339 Tn7 transposon, 515, 520-521 tolC, 385 Topoisomerase
I, 405,408-409, 827, 828 II, 475, 68O
cleavage sites in scs and scs ' , 46-47
in detection of DNA domains containing single-copy genes, 29-31
and DNase-I-hypersensitive sites, 26-28, 46
inhibitors. See Chromomycin; VM-26
and MARs/SARs, 25-29, 32, 755, 763
and pairing of homologous chromosomes, 561-563
phosphorylation by CKII, 621 stimulator. See Distamycin
IV, 385-386 Topoisomer distribution, ssn6 vs.
tupl mutants, 240 Topology and pairing of
homologous chromosomes, 553-564
Tramtrack, DNA-binding domain, 141-143, 146
trans-Acting factors and regula- tion, 5, 32-33, 225, 491, 593, 820-821,824-825
trans-Activator VP16. See VP16 Transcription. See also Enhancer;
Gene expression; Promoter; RNA polymer- ase; Suppressors; Tran- scription factors
activation. See also Domains; Enhancer; Transcription, antirepression
chromatin structure effect, 1- 4, 63-70, 824-826. See also Chromatin; Histones; Nucleosomes
hsp26 as preset gene, 83-95 preset genes vs. remodeling,
83, 88 role of (CT) n elements, 89,
94 coactivators and TAFs, 179-
184, 202 effect of activators on
preinitiation complex as- sembly, 199-202
by GAL4 derivatives. See GAL4
hormone receptors in. See Estrogen receptor; Glucocorticoid receptor; Progesterone receptor; Steroid receptor
MCB-directed. See MCB Oct-2 vs. Oct-1 in VP16-
induced complex, 167- 176
virus-inducible in IFN-fi, 73- 80
yeast SNF/SWI role, 257-262 allele-specific. See Imprinting antirepression, 205-213,825 attenuation in VSG gene, 109-
I10 and combinatorial control, 73-
80, 167-176, 832-834 "competence" and DNase
sensitivity. See DNase I sensitivity of chromatin
"concerted action model," 38, 42- 43
DNA methylation role. See Im- printing; Methylation of DNA
and DNA nicking, 32 and DNA repair, 612-613, 615,
629-630 ecdysone in regulation, 491-493 effect of chromatin assembly,
233 effect of DNA replication and
amplification, 490- 493
homeodomain proteins in regulation. See Homeodomain proteins
and inactivation in X chromosome. See Chromosome, X
inhibitors. See Actinomycin D; cr Amanitin
initiation. See also Preinitiation complex; RNA polymerase
DNA bending in, 115-122
S U B J E C T INDEX 859
to elongation cycling, role of RNA polymerase phosphorylation, 187- 197
and interchromosome domain compartment, 786-788
and ~. replication initiation, 389- 4OO
localization and export of trans- cripts. See Nucleus
long-range control, 210-211, 821-823. See also En- hancer; Insulator ele- ments; LCR; Transcrip- tion, repression and silencing
in perichromatin fibrils, coor- dination with splicing, 785-786, 799-804
and processing. See pre-rRNA processing and snur- posomes; Splicing
repression and silencing, 94, 159, 437, 441,822, 824. See also Heterochromatin; In- sulator elements
cell-stage specific inactivation of lysozyme gene, 39-40
chromatin compaction and electric forces role, 786- 788
chromatin- or Hi-mediated, counteracting. See Tran- scription, antirepression
chromatin structure and nucleosome positioning roles, 83,213-222,233, 237-244, 250-255, 743- 744, 823-826. See also Histones; Nucleosomes
g]obin genes, 11 mating-type genes in yeast,
248-255, 733, 737-740, 743-744, 824, 829-830
a-cell-specific and a2 repres- sor, 237-244
E and I silencers, 444 silencer as origin of DNA
replication, 443-454 methylation-mediated. See
Methylation of DNA pairing-sensitive repression of
white minigene, 52-53 pre- and postinduction of IFN-
[~, 73-74 silencers in TCR loci sequence,
346 sub-telomeric DNA modifica-
tion in attenuation, 108- 110
telomeric silencing, 107-109, 249-255, 421-422, 427, 725, 733, 743-744, 830
role in control of yeast S-phase- specific genes, 638-639
role of domain organization of DNA in control. See Domains
Transcription factors, 5, 167, 187, 199, 786, 821-822, 827- 828, 832-834. See also spectfic factors
access to DNA chromatin structure and
nucleosome/histone role, 5, 63-70, 217-218, 222, 225-234, 533
~t enhancer role, 97-102 and DNA methylation, 281-282 HLH and b/HLH/Z motifs, 123,
126-128 ligand-modulated. See Estrogen
receptor; Glucocorticoid receptor; Nuclear non- steroidal receptors; Steroid receptor
and model for trans-inactivation. See trans-Inactivation of brown gene
promoter-selective, 179-184 role in DNA replication, 403-412 role of sequence-specific in
antirepression. See GAGA factor; Spl; VP16, GAL4-VP16
with same DNA-binding specificity, mechanisms for differential regula- tion of transcription, 167-176
sequence-specific DNA recogni- tion, 141-146
stereochemistry of specific DNA mteractions, 133-139
synergistic interactions, 77-80, 822
TFIIA, 125, 187-189, 199, 827- 828
TFIIB, 192, 195, 199, 821-822 as target of acidic activators,
2O0-2O2 and TBP interaction, 188-189
TFIID, 64, 93-94, 123, 187-188, 195, 199, 202, 259, 821- 822,827-828. See also TAFs; TATA box, -binding protein
coactivator activity and TAFs, 180-184
TFIIE, 192, 195, 199, 821-822 TFIIF, 199, 821-822, 827-828
and polymerase association with preinitiation com- plex, 187-190, 192, 195
TFIIH, 199, 827 DNA helicase activity, 193,
197, 262 ERCC3 as subunit, 611,627,
629 kinase activity, 191-193, 195
TFIIJ, 195, 199
TFIIIA access to nucleosomal DNA,
225-234 zinc finger, 134, 141,225
TFIIIB TAFs, 182 X-ray crystallographic studies of
TBP, Max, and HNF- 3~fork head, 123-130, 826-827
Transcripts. See Nucleus; RNA, transcripts
Transferrin-binding protein (TFBP) and receptor, antigenic variation, 110- 111
Transformation P-element-mediated. See P ele-
ment of trypanosomes, 105
Transgenic mice and chromatin structure effect
on transcription, 1-3 generating with YACs covering
tyrosinase gene, 55-61 and globin gene switching, 7-12 and imprinting, 289, 291-294 and transcription regulatory
units for lysozyme gene, 37, 40-43
Transgenic yeast strains with I- Sce I sites for mapping, 358, 360
trans-Inactivation of brown gene, 577-583
Translational positioning of histone octamer core, 226-228, 231-232
Translocations. See also Genomic sequencing
FISH for cytogenetic analysis, 772-773
Transposases. See P element Transposition. See also P element
of phage Mu, target site prefer- ence at DNA strand transfer, 515-522
of Tyl and Ty3, integration target, 539-540
Transposons and retrotransposons, 52. See also bluetail transposon; P element; Tn7 transposon; Tyl and Ty3
copy number and regulation of position-effect variega- tion in heterochromatin, 592-594
enhancer trap. See Enhancer, trapping
trans-Splicing. See Splicing Transvection and communication
within and between domains, 33
Trithorax group genes, 49-50, 53 tRNA genes, 241, 243, 360, 370,
687
860 SUBJECT INDEX
TRPIARS1 minichromosomes and retroviral DNA integra- tion target, 534
Trypanosomes control of antigenic variation,
105-112 and telomere length, 107-109,
720 Trypsin inhibitor. See BPTI Trypsinogen gene family in TCR
sequence, 346-347 TS, 664 Tumor initiation and progression.
See Gene amplification Tumor suppressor genes. See p53;
Rb-dependent cell cycle arrest
Tyl and Ty3, integration targets, 539-540
Tyl-17, 421 Tyrosinase gene, YACs covering,
55-61 Tyrosine hydroxylase gene and im-
printing, 307-308
U
Ubx gene. See Bithorax complex Unidirectional and bidirectional
replication in )~, 389-400 URA3 gene and telomeric repres-
sion, 249, 733 UV-irradiated DNA, recombina-
tion and repair, 525, 529, 625. See also Recombina- tion; Repair of DNA; Xeroderma pigmentosum
UV-mediated cross-linking. See Cross-linking
UvrABC excision repair enzymes, 528, 605, 630. See also (A)BC excinuclease
V
V (variable) gene segment. See TCR
Variable (V) gene segment. See TCR
Variant surface glycoprotein (VSG) gene, antigenic variation, 106-112
Variegating phenotype. See Heterochromatin
VCAF. See HCF Vertebrates
development and DNA methyla- tion. See Imprinting
function of DNA methylation in, 281-284
Viral machinery as probe of chromatin structure. See Retroviral DNA integra- tion
Viral oncogenes and gene amplification, 648, 651- 652
Viral sequence proliferation, DNA methylation role, 283
Virus-inducible enhancer complex for IFN-~ gene and HMG I(Y), 73-80, 834
Vitamin D 3 receptor, 133-134, 136 Vitellogenin
B1 gene and nucleosomes, 94 probe, oligonucleosome
solubility, 16, 19-22 VM-26, 26-31 Vmw65. See VP16 VP16
acidic activator region interac- tion with TFIIB, 200- 201
GAL4-VP16 in antirepression/activation of
transcription, 206-207, 209-211,213-214, 219- 222
and DNA replication, 409-412 -induced complex of HSV, com-
binatorial control of transcription, 167-176
VSG. See Variant surface glycoprotein gene
W
Water molecules in hydration sites, residence times, 151-152, 155-156
white gene. See Drosophila Writhe, 117, 121-122
X
Xce (X chromosome controlling ele- ment) locus, 319-320
X chromosome. See Chromosome Xenopus, 488
GV of oocytes and pronuclei, snurposomes and coiled bodies in, 747-753
and licensing factor model for coupling cell cycle to replication, 639
recombinant nucleosome core particles and globular domain of H1, 266, 270- 271
rRNA gene-containing nucleosome and tran- scription factor access, 225-234
site-specific replication initia- tion, role of nuclear orga- nization, 478-484
TFIIIA, 134, 141, 225-234 vitellogenin B 1 gene. See Vitel-
logenin
Xeroderma pigmentosum (XP), complementation groups and excision repair, 605- 615,625-631
X inactivation and X/C (X in- activation center). See Chromosome, X
X I S T / X i s t gene, 813, 816 noncoding RNA transcript, 320 and X inactivation, 294, 303,
317-321,831 X-linked genes. See Chromosome,
X XP and XPAC protein. See
Xeroderma pigmentosum X-ray crystal structure, 826-827
FIS, 505 HhaI, 331-337 MATa2 homeodomain/DNA,
159-165 nucleosomes and histone oc-
tamers, 265-271,275- 276
receptor DNA-binding domains, 133-139, 141, 143-146
reverse transcriptase and Klenow fragment, 495- 501
in study of protein hydration, 149, 151, 153-155
TBP, Max, and HNF-3/fork head, 123-130, 826- 827
Tramtrack DNA-binding domains, 141-143, 146
X-ray-induced DNA nicking and transcription sensitivity, 32
X-ray-induced recombination and repair, 567. See also Recombination; Repair of DNA
Y
YACs (yeast artificial chromosomes), 31-32, 642, 767
amplifiable, 55, 57-58 covering tyrosinase gene for gen-
erating transgenic mice, 55-61
DNA introduction into cells, 55 in mapping, 349,353
C. elegans, 368 human genome, MegaYACs
and YAC to YAC Alu- PCR hybridization, 377- 382
Y chromosome. See Chromosome Yeast, 66, 829-830. See also
Abfl/ABF1; ARS; cdc mutations, genes, and proteins; GAL4; Mini- chromosomes
SUBJECT INDEX 861
a-cell-specific gene and a2 repressor. See a2 repres- s o r
artificial chromosomes. See YACs
CDC9 and cdc17 + gene product homology with DNA ligases, 619
checkpoint control of cell cycle. See RAD proteins, RAD9
chromatin structure, dam methylase in study of, 251
excision repair genes and proteins, 611-613, 627
HM loci. See HM loci and repres- sion
MATal protein, 159, 161,165 MATch2 homeodomain, structure
and DNA-hinding specificity, 159-165
MCM1 protein, 159, 162, 165 Saccharomyces cerevisiae
centromere/kinetochore, 669- 675, 681-683
chromosome structure and function in mitosis, 677- 684
heterochromatin, 679 position effects and silencing
of genes, 248-255 mapping
genetic, 363-364 physical, 358, 360, 363-364 restriction, resolution-
completeness profile, 351-352
mating-type interconversion, 443,462-463
pairing of homologous chromosomes, 553-554
RAD51 and RAD52 genes for recombination/repair, 567-575
replication, 386 and A R S element function,
409, 415-422, 425-433, 435-436
initiator protein ORC, 436- 441
position effects on origin, 421-422, 426-427
transcriptional silencer as origin, 443-454
sequencing genome, 357-365 GC periodicity, 363,365
SNF/SWI proteins in tran- scriptional activation, 257-262
Schizosaccharom yces pombe centromere structure and
function, 687-694 DNA replication and coordina-
tion with mitosis, 639- 642
mating-type interconversion and imprinting, 457-464
position effects at centromere, 249
RAD51 gene for recombina- tion/repair, 569-575
telomere length, 720, 733-734, 737-740, 744
telomere replication, 725-731 telomeric repression and posi-
tion effects, 249-255, 421-422,427, 725, 733, 743-744
transcriptional control of S- phase-specific genes, 638-639
Tyl and Ty3, integration targets, 539-540
yellow gene. See Drosophila YOYO-1 and YOYO/MG staining
of loop bodies, 758-763 yp-1 enhancer blocking, 47-48
Z
zeste protein and topological orga- nization of domains, 33
~-~ region of Neurospora and DNA methylation, 323-329
Zinc fingers and zinc-stabilized motifs
of ATF-2, 76 of DNA-binding domains of
hormone receptors, 134, 141, 143-146
of DNA-binding domain of Tram- track, 141-143, 146
of TFIIB, 188 of TFIIIA, 134, 141,225
Zipper proteins, 123, 126-128 Z X D A / B genes and X inactivation,
316-317 Zygotic meiosis and pairing of
homologous chromosomes, 553, 558- 560, 562
Zygotic sporulation, 459