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

How do distal enhancers find their target genes?

1. What is the mechanism that allows a distal enhancer to exert its effect on a remote promoter?

2. What is the process that prevents an enhancer to affect a non-target promoter?

Lobanenkov VV, Felsenfeld G, Tilghman S, Bartolomei, Groudine, Corces… Schleif RF, Ptashne M, Schaffner W, Thanos D, Dean A. …

Felsenfeld & Groudine, Nature 2003

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H2A , H2B , H3 and H4

Bolzer et al., PLoS Biol. 2005

Chromatin domains in the genome

Hawkins et al., Cell Stem Cell 2010Lister et al., Nature 2009

Chromosomes are organized into large domains, replication timing, and lamina association

Replication Timing

Lamina Association

H3K9me2 Modification

Peric-Hupkes … van Steensel, (2010) Mol Cell 38 (4) pp. 603-13

Hiratani … Gilbert (2009) Genome Research

FISH analysis of genomic loci

Chromosome painting

Chromosome painting analysis of interphase nuclei reveals chromosome territories

Bolzer et al., PLoS Biol. 2005

Sachs et al, PNAS 1995; 92:2710; Munkel & Langowski Phys Rev 1998Jhunjhunwala et al. Cell 2008 : Iyer et al. BMC Biophysics 2011 4:8;

Models of Chromosomal Organization

Chromosome conformation capture

Dekker, Trends in Biochemical Sciences, 2003

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)