Download Chromatin Structure & Genome Organization

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 15100Kbp 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 are
Just four subtypes.
They're conserved
evolutionarily.
• Two each
Of each histone
Do their thing.
Forming
Just like beads upon a
string.
• H1
Binds the complex.
And it inhibits new
transcription
And the creation
Of new mRNA.
Transcriptional Regulation by Histone
Modification
• Histone acetyltransferase is component of transcriptional
activation complexes
H1 Promotes Nucleosome Compaction
-H1
+H1
• H1 function thought
to be regulated by
phosphorylation on
N and C terminal
tails
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 islan
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
23 – 9bp Repeats
Mouse Satellite DNA
Repeating unit given by restriction enzyme digestion
4 Imperfect Repeating Units
VNTRs in DNA Fingerprinting