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 longrange interaction, with some interacting
with as many as 20 distal fragments.
Expressed TSSs interact with slightly
more fragments as compared to nonexpressed 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
Fix Cells Digest
Ligate
Chromatin
Biotin Labeling
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
Compartment B
Compartment A
Lieberman-Aiden et al., 2009
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