Feb 24, 2016
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/