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