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Chromatin Structure & Genome Organization
Overview of Chromosome Structure• Nucleosomes
– ~200 bp DNA in 120Å diameter coil– 3.4Å/bp x 200 = 680Å– 680/120 = 5X compaction
• 30nm fiber– Coil of nucleosomes w/ 6/turn– 1200bp/120Å vs 4080Å = 34X
compaction• Chromatin loops
– 30nm fiber is looped into 15-100Kbp loops
– 7-8 loops form rosette w/ bases of loops attached to central core of scaffold proteins
– 300Å/rosette, 800Kbp/rosette = 800kbp/300Å vs 2720000Å 9000X compaction
Nucleosomes
• Core of 8 proteins, 2 of each– H2A– H2B– H3– H4
• 166 bp of DNA• ~40bp between
successive nucleosomes
Nucleosomes
• DNA associated with individual nucleosomes determined by DNAse I digestion
Nucleosome
• Each nucleosome contains 1 linker histone – H1
• Linker histones can vary with cell types and differentiation states
Histone Post-translational Regulatory Modifications
• Acetylation • Phosphorylation
The Histone Song (To the tune of "Flintstones")
With Accompaniment
• Histones!Meet the Histones!They're a basic protein family.
• There areJust four subtypes.They're conserved evolutionarily.
• Two eachOf each histoneDo their thing.FormingJust like beads upon a string.
• H1Binds the complex.And it inhibits new transcriptionAnd the creationOf new mRNA.
Transcriptional Regulation by Histone Modification
• Histone acetyltransferase is component of transcriptional activation complexes
H1 Promotes Nucleosome Compaction
• H1 function thought to be regulated by phosphorylation on N and C terminal tails
-H1
+H1
Heterochromatin vs Euchromatin• Constitutive heterochromatin
– Never transcribed DNA
• Facultative heterochromatin– DNA regions that can be switched between
heterochromatin and euchromatin states– X inactivation
• Chromo domain proteins– Bind to DNA keeping in heterochromatin state
• Polycomb protein family in Drosophila
Heterochromatin vs Euchromatin• Modifications to histones and DNA direct formation of
heterochromatin•Deacetylation of H4•Methylation of H3
•Methylation of CpG islands
Loops & Chromosome Scaffolds• Chromosome scaffold
– Proteins at base of loops– Potentially regulate formation of loops and/or regulate global gene
expression
• Components– DNA topoisomerase II– SMC proteins– HMGA
• DNA elements– S/MARS
• Sequences of DNA to which scaffold proteins bind
– LCR• DNA elements known to regulate expression of large regions of DNA containing
multiple genes
– Boundary elements• scs elements flank puffs in Drosophila polytene chromosomes
Chromosome Loops
Chromosome Structure: The Metaphase Chromosome
Centromeres• DNA sequence
– Repetitive DNA elements– Constitutive
heterochromatin
• Protein components– CENP-A, B & C
Centromeres
• Repetitive DNA of mammalian centromeres satellite DNA – 171 bp unit– Several specific unit
sequences– Multiple repeats of these
units form arrays
Centromeres• Centromere of S. cerevisiae
– CEN DNA is 125bp element – 3 regions - CDE I, II, & III– CDE's bound by special histone
and other proteins and direct attachment of microtubule
Telomeres
Genome Organization
• Sequence composition– Unique sequences
• Genes
– Low copy # elements• rRNA, 5S, tRNA genes
– High copy # repetitive DNA• Retroelements
– LINEs– SINEs
• Simple Sequence DNA – Minisatellites (VNTR)– Microsatelites
Retrotransposons, Retroelements & Transposons
Mouse Satellite DNA
Repeating unit given by restriction enzyme digestion
4 Imperfect Repeating Units
23 – 9bp Repeats
VNTRs in DNA Fingerprinting