Analysis of Higher Order Chromatin Structure

Analysis of Higher Order Chromatin Structure

Current Topics of Genomics and Epigenomics

Outline Motivation for analysis of higher order

chromatin structure Methods for studying long range

chromatin interactions Topological domains Functional implications of topological

domains Break for 5’ Paper discussion

Chromosome conformation capture carbon copy (5C)

Dostie et al., 2006

Chromosome conformation capture carbon copy (5C)

Dostie et al., 2006

Identification of long range chromatin interaction in the human cells by 5C

Sanyal et al. Nature 2012 (DOI:10.1038/nature11279)

Network of long range chromatin interaction at promoters

Sanyal et al. Nature 2012 (DOI:10.1038/nature11279)

Network of long range chromatin interaction at promoters 50% of TSSs display one or more long-

range interaction, with some interacting with as many as 20 distal fragments.

Expressed TSSs interact with slightly more fragments as compared to non-expressed TSSs

Out of all distal fragments interrogated, 10% interacted with one or more TSS, with some interacting with more than 10.

gene–element interactions are not exclusively one-to-one, and multiple genes and distal elements can assemble in larger clusters

Sanyal et al. Nature 2012 (DOI:10.1038/nature11279)

Hi-C for genome-wide analysis of higher order chromatin structure

Lieberman-Aiden et al., 2009

Hi-C for genome-wide analysis of higher order chromatin structure

Hi-C vs. FISH

Mouse ES cells (from 433 Million Reads) Dixon et al., Nature, 2012

The genome is composed of megabase sized topological domains

Hi-C data reveals strong local chromatin interaction domains

Dixon et al. Nature 2012

The genome is composed of megabase sized topological domains

Topological Domains in Mouse ES cells

N = 2200

Properties of the topological domains Topological domains are stable between different cell

types.

hESC

IMR90

Dixon et al. Nature 2012

Properties of the topological domains Topological domains are stable between different cell

types. Topological domains are conserved between species

Dixon et al. Nature 2012

Observations Hi-C analysis reveals that the mammalian genome

consists of mega-base sized topological domains (also known as TADs).

Topological domains are stable across cell types and largely preserved during evolution, suggesting that they are a basic property of the chromosome architecture.

Higher order structure of the topological domains

Lieberman-Aiden et al., 2009

Compartment A

Compartment B

Topological Domains vs. Compartment A & B

Replication Timing Data

3-D model of a chromosome

Structure model of the mouse Chr 2 is reconstructed using Bayesian inference approach

This chromosome appears to take a helical configuration

Topological domains in compartment A and B are located on different side of the chromosomal structure Red: compartment A domains Blue: compartment B domains

Hu et al., PLoS Comp Bio. 2013

3-D model of a chromosome

Heterochromatin and euchromatin are located on different faces of the chromosomal structure (Red: H3K9m3 enriched domains; Blue: H3K9me3 depleted domains)

Hu et al., PLoS Comp Bio. 2013

3-D model of a chromosome

Lamina B binding sites are clustered on one face of the chromosomal helical structure

Red: enriched for Lamina B binding sites

Blue: depleted for Lamina B binding

Hu et al., PLoS Comp Bio. 2013

3-D model of a chromosome

Transcriptionally active domains are located on one face of the chromosomal helical structure

Red: enriched for RNA polymerase II binding sites

Blue: depleted for RNA polymerase II binding sites

Hu et al., PLoS Comp Bio. 2013

Functional implications of topological domains Prediction: Partitioning of the genome

into topological domains would naturally restrict the enhancers to selective promoters

Shh and its distal enhancer are located in the same topological domain

Enhancer

How do topological domains form?

The topological domain boundaries coincide with heterochromatin domain boundaries

Dixon et al. Nature 2012

What protein factors bind to the topological domain boundaries?

Kim et al. PNAS 2011

Not all CTCF binding sites are at the boundaries

Topological domain boundaries are also enriched for housekeeping genes

Further Reading Reviews

Giacomo Cavalli & Tom Misteli, “Functional implications of genome topology”, Nat Struct Mol Biol, 2013 vol. 20 (3) pp. 290-9

Michael Bulger, Mark Groudine, “Functional and Mechanistic Diversity of Distal Transcription Enhancers”, Cell, 144 (2011) 327-339. doi:10.1016/j.cell.2011.01.024

T Cremer, C Cremer, “Chromosome territories, nuclear architecture and gene regulation in mammalian cells”, Nat Rev Genet, 2001 vol. 2 (4) pp. 292-301

Tom Misteli, “Beyond the sequence: cellular organization of genome function”, Cell, 2007 vol. 128 (4) pp. 787-800

Elzo de Wit, Wouter de Laat, “A decade of 3C technologies: insights into nuclear organization”, Genes & Development, 2012 vol. 26 (1) pp. 11-24

Sjoerd Holwerda, Wouter de Laat, “Chromatin loops, gene positioning, and gene expression”, Front. Gene., 2012 vol. 3 pp. 1-13

ChIA-PET (chromatin interaction analysis by paired-end tags)

Fullwood … Ruan, Nature 2009 vol. 462 (7269) pp. 58-64