Crosslink YLyse & Sonicate

IP Reverse crosslinks

Total Reverse crosslinks Amplify

Amplify

Sequence

Sequence

Immuno-precipitation

Other controls for IP(e.g., no antibody, non-

specific antibody)

ChIP-seq

[Zhang, et al., 2011, Biometrics]

Transcriptional regulation by nucleosome and histone modification

Nucleosome positioning is mainly repressive

TF

TF

TF target site

Transcription factor binding sites (TFBSs) are likely to be nucleosome-depleted

TFBSs tend to be nucleosome-depleted.Motif sites that are unbound in our condition but bound in other conditions also tend to be nucleosome depleted.Motif sites that are always unbound do not have nucleosome-depletion property.

Yuan et al. 2005

Genome-wide nucleosome positions

Yeast Human

Genome-wide nucleosome positions can be identified by MNase based tiling array or DNA sequencing methods

Most promoters contain nucleosome depleted regions before TSS.

Lee et al. 2007 Schones et al. 2008

Transcriptional regulation by nucleosome and histone modification

Nucleosome positioning is mainly repressive

Histone modification can be either active or repressive

TF

TF

TF target site

TF

TF

Ace

TFH3K27me3

H3K9ac

TF

Correlation between gene expression and different histone modification patterns

Barski et al. 2007

Histone code hypothesis“… multiple histone modifications, acting in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream functions …” ― Strahl and Allis,

Nature, (2000)

Summary

• Exciting time to work on epigenetics– NIH Epigenetic Roadmap– Compendium of epigenetic state for many tissues

• Lots of population-based science to be done: development, disease, aging, etc.

• How it regulates expression it still not clear• How genetic alterations are involved is not

clear at all

UCSC Genome Browser:http://genome.ucsc.edu/