Analysis of Higher Order Chromatin Structure

1. Current Topics of Genomics and Epigenomics Analysis of Higher Order Chromatin Structure

2. 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

3. How do distal enhancers find their target genes? What is the mechanism that allows a distal enhancer to exert its effect on a remote promoter? What is the process that prevents an enhancer to affect a non-target promoter? Schleif RF, Ptashne M, Schaffner W, Thanos D, Dean A. … Lobanenkov VV, Felsenfeld G, Tilghman S, Bartolomei, Groudine, Corces…

4. ? H2A , H2B , H3 and H4 Felsenfeld & Groudine, Nature 2003 Bolzer et al., PLoS Biol. 2005

5. Chromatin domains in the genome Hawkins et al., Cell Stem Cell 2010 Lister et al., Nature 2009

6. Chromosomes are organized into large domains, replication timing, and lamina association H3K9me2 Modification Replication Timing Lamina Association Peric-Hupkes … van Steensel, (2010) Mol Cell 38 (4) pp. 603-13 Hiratani … Gilbert (2009) Genome Research

7. FISH analysis of genomic loci

8. Chromosome painting

9. Chromosome painting analysis of interphase nuclei reveals chromosome territories Bolzer et al., PLoS Biol. 2005

10. Models of Chromosomal Organization Sachs et al, PNAS 1995; 92:2710; Münkel & Langowski Phys Rev 1998Jhunjhunwala et al. Cell 2008: Iyeret al. BMC Biophysics 2011 4:8;

11. Chromosome conformation capture Dekker, Trends in Biochemical Sciences, 2003

12. Chromosome conformation capture carbon copy (5C) Dostie et al., 2006

13. Chromosome conformation capture carbon copy (5C) Dostie et al., 2006

14. Identification of long range chromatin interaction in the human cells by 5C Sanyal et al. Nature 2012 (DOI:10.1038/nature11279)

15. Network of long range chromatin interaction at promoters Sanyal et al. Nature 2012 (DOI:10.1038/nature11279)

16. 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)