Organization of Genetic Information in Cells

“flow” of genetic information

eukaryotic

Organization of DNA within the nucleus:
1. Compacts and organizes DNA
2. Regulates accessibility of DNA to trans-acting factors

chromatin

Repeating unit of chromatin

nucleosome

small, basic proteins
globular domain, extended N-terminal tails

histones

Histone H1 permits what-order chromatin structure

higher

Histone PTMs regulate what expression: Repressed vs. Active Chromatin

gene

Histone PTMs regulate gene expression: Repressed vs. Active Chromatin
1. Serve as docking sites to recruit what proteins.

nonhistone

Histone PTMs regulate gene expression: Repressed vs. Active Chromatin
2. Alter the way histones of neighboring what interact

nucleosomes

“distinct what modifications, on one or more tails, act sequentially or in combination to form a 'what code' that is, read by other proteins to bring about distinct downstream events”

Histone Code Hypothesis

How are histone PTMs controlled and how do they control gene expression?

Writers, Readers and Erasers

Catalyze addition of modification to histone

Writers

histone methyltransferase

histone acetyltransferase

Writers

Catalyze removal of modification to histone

Erasers

histone demethylase

histone deacetyltransferase

Erasers

Bind specific histone modifications and direct downstream functions

Readers

Readers: Have protein what that recognize specific modifications

domains

most DNA becomes dispersed after mitosis

euchromatin

some remains condensed

heterochromatin

can be transient or maintained

heterochromatin

X inactivation (Barr body)

heterochromatin

formation of heterochromatin

non-coding RNAs to direct (guide) what of DNA via deacetylation and methylation

inactivation

contains a chromodomain that binds H3K9 methyl

HP1 (Heterochromatin Protein 1)

How can we identify a specific sequence of DNA within a chromosome?

FISH: fluorescence in situ hybridization

Anatomy of a Chromosome

site of kinetochore; microtubule attachment specified by a centromere specific variant of histone H3

centromere

Anatomy of a Chromosome

repeated sequence at chromosome end; protects ends from degradation

telomere

antibody against telomeric protein

immunofluorescence (IF)

telomere repeat probe

fluorescence in situ hybridization (FISH)

short, repeated sequences

Satellite DNAs

Highly Repeated DNA Sequences – represent about what % of total DNA

1-10

Highly Repeated
DNA Sequences
Satellite DNAs

heterochromatin

The 3D Organization of the Genome

more active (more protein-coding genes)

Chromosome 19

The 3D Organization of the Genome
less active (fewer protein-coding genes)

Chromosome 18

silent genes

Heterochromatin

active genes

Euchromatin

Chromosome territories

at periphery

Heterochromatin

Chromosome territories

at interior

Euchromatin

transcription initiation at RNA pol # promoters

II

activate or repress many bound to one promoter each factor usually binds many promoters

Gene specific transcription factors

multiprotein complexes that “move” or exchange nucleosomes (often ATP dependent)

Chromatin remodelers