The genetic material is compacted to a limited volume

Condensing viral genomes into their coats

The bacterial genome is negatively supercoiled

• with ~100 independently negatively supercoiled indipendent domains

• an average density of supercoiling of ~1 turn/100 bp.

Domain of a chromosome may refer either to

•a discrete structural entity defined as a region within which supercoiling is independent of other domains;

• an extensive region including an expressed gene that has heightened sensitivity to degradation by the enzymeDNAase I.

eukaryotic DNA

DNA of interphase chromatin is negatively supercoiled into independent domains of ~85 kb. Nuclear matrix is a network of fibers surrounding and penetrating the nucleus. Metaphase chromosomes have a protein scaffold to which the loops of supercoiled DNA are attached.

Scaffold of a chromosome is a proteinaceous structure in the shape of a sister chromatid pair, generated when chromosomes are depleted of histones.

Metaphase chromosomes have a protein scaffold to which the loops of supercoiled DNA are attached.

Histone-depleted chromosomes consist of a protein scaffold to which loops of DNA are anchored. Photograph kindly provided byUlrich K. Laemmli.

MAR (matrix attachment site; also known as SAR for scaffold attachment site) is a region of DNA that attaches to the nuclear matrix.

DNA is attached to the nuclear matrix at specific sequences called MARs or SARs. The MARs are A·T-rich but do not have any specific consensus sequence.

Centromeres have short DNA sequences in S. cerevisiae CEN elements are identified in S. cerevisiae by the ability to allow a plasmid to segregate accurately at mitosis. CEN elements consists of short conserved sequences CDE-I and CDE-III that flank the A·T-rich region CDE-II. The CBF3 protein complex that binds to CDE-III is essential for centromeric function.

Centromeres in higher eukaryotic chromosomes contain large amounts of repetitious DNA.

Telomere is the natural end of a chromosomeis required for the stability of the chromosome end

Its DNA sequence consists of a simple repeating unit with a protruding single-stranded end that may fold into a hairpin.

The protein TRF2 catalyzes a reaction in which the 3 repeating unit of the G+T-rich strand forms a loop by displacing its homologue in an upstream region of the telomere

A nucleosome contains ~200 bp of DNA, 2 copies of each core histone (H2A, H2B, H3, H4), and 1 copy of H1. DNA is wrapped around the outside surface of the protein octamer.

Micrococcal nuclease is an endonuclease that cleaves DNA; in chromatin, DNA is cleaved preferentially between nucleosomes.

Micrococcal nuclease releases individual nucleosomes from chromatin as 11S particles.

>95% of the DNA is recovered in nucleosomes or multimers when micrococcal nuclease cleaves DNA of chromatin. The length of DNA per nucleosome varies for individual tissues in a range from 154-260 bp.

Linking number paradox describes the discrepancy between the existence of -2 supercoils in the path of DNA on the nucleosome compared with the measurement of -1 supercoil released when histones are removed.

The histone octamer has a kernel of a H32·H42 tetramer associated with two H2A·H2B dimers. Each histone is extensively interdigitated with its partner.

All core histones have the structural motif of the histone fold. N-terminal tails extend out of the nucleosome.

Hypersensitive site is a short region of chromatin detected by its extreme sensitivity to cleavage by DNAase I and other nucleases; comprises an area from which nucleosomes are excluded.

A domain containing a transcribed gene is defined by increased sensitivity to degradation by DNAase I.

Euchromatin are chromosome regions less packed occupies most nuclear regions and represents the active structure

Heterochromatin is nucleated at a specific sequence and the inactive structure propagates along the chromatin fiber. Genes within regions of heterochromatin are inactivated. Because the length of the inactive region varies from cell to cell, inactivation of genes in this vicinity causes position effect variegation. Similar spreading effects occur at telomeres and at the silent cassettes in yeast mating type.

RAP1 initiates formation of heterochromatin in yeast by binding to specific target sequences in DNA. The targets of RAP1 include telomeric repeats and silencers at HML and HMR. RAP1 recruits SIR3/SIR4, which interact with the N-terminal tails of H3 and H4.

In eukariotes DNA can be modified although with important differences with respect

to procariotes

Hemi-methylated site is a palindromic sequence that is methylated on only one strand of DNA. Maintenance methylase adds a methyl group to a target site that is already hemimethylated. Methylase is an enzyme that adds a methyl group to a substrate, which can be a small molecule, a protein, or a nucleic acid.

De novo methylase adds a methyl group to an unmethylated target sequence on DNA. Fully methylated site is a palindromic sequence that is methylated on both strands of DNA.

Imprinting describes a change in a gene that occurs during passage through the sperm or egg with the result that the paternal and maternal alleles have different properties in the very early embryo. May be caused by methylation of DNA.

Chromatine structure controls gene expressionin eukariotes

The pre-emptive model for transcription of chromatin proposes that if nucleosomes form at a promoter, transcription factors(and RNA polymerase) cannot bind.

If transcription factors (and RNApolymerase) bind to the promoter to establish a stable complex for initiation, histones are excluded.

Chromatin remodeling describes the energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription.

There are several chromatin remodeling complexes that use energy provided by hydrolysis of ATP. The SWI/SNF, RSC, and NURF complexes all are very large; there are some common subunits. A remodeling complex does not itself have specificity for any particular target site, but must be recruited by a component of the transcription apparatus.

Hormone receptor and NF1 cannot bind simultaneously to the MMTV promoter in the form of linear DNA, but can bind when theDNA is presented on a nucleosomal surface.

HAT (histone acetyltransferase) enzymes modify histones by addition of acetyl groups; some transcriptional coactivators have HAT activity.

HDAC (histone deacetyltransferase) enzymes remove acetyl groups from histones; they may be associated with repressors of transcription.

Coactivators may have HAT activities that acetylate the tails of nucleosomalhistones.

Histone acetylation is associated with activation of gene expression. Deacetylated chromatin may have a more condensed structure.

A repressor complex contains three components: • a DNA binding subunit,

• a corepressor,

• a histone deacetylase.

Polycomb and trithorax are antagonisticnrepressors and activators

Polycomb group proteins (Pc-G) perpetuate a state of repression through cell divisions. The PRE is a DNA sequence that is required for the action of Pc-G. The PRE provides a nucleation center from which Pc-G proteins propagate to maintain an inactive structure. No individual Pc-G protein has yet been found that can bind the PRE. Trithorax group proteins antagonize the actions of the Pc-G.

LCR is the locus control region that is required for the expression of several genes in a domain.

An LCR is located at the 5 end of the domain and consists of several hypersensitive sites.

Insulators block enhancer actions. Insulator between two sites will prevent an activating or inactivating effect passing from one to the other.

Special structures, called scs and scs (specialized chromatin structures, are found at the ends of the bands.

insulator between two sites will prevent an activating or inactivating effect passing from one to the other. LCR is the locus control region that is required for the expression of several genes in a domain. MAR (matrix attachment site; also known as SAR for scaffold attachment site) is a region of DNA that attaches to the nuclear matrix.

Gene expression is associated with demethylation