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Immuno -precipitation

Y. Immuno -precipitation. Total. Reverse crosslinks. Sequence. Amplify. Crosslink. Lyse & Sonicate. Reverse crosslinks. Other controls for IP (e.g., no antibody, non-specific antibody). IP. Amplify. Sequence. ChIP-seq. [Zhang, et al., 2011, Biometrics]. TF. TF.

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Immuno -precipitation

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  1. Y Immuno-precipitation Total Reverse crosslinks Sequence Amplify Crosslink Lyse & Sonicate Reverse crosslinks Other controls for IP (e.g., no antibody, non-specific antibody) IP Amplify Sequence

  2. ChIP-seq [Zhang, et al., 2011, Biometrics]

  3. TF TF Transcriptional regulation by nucleosome and histone modification Nucleosome positioning is mainly repressive TF target site

  4. 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

  5. Genome-wide nucleosome positions Genome-wide nucleosome positions can be identified by MNase based tiling array or DNA sequencing methods Most promoters contain nucleosome depleted regions before TSS. Yeast Human Lee et al. 2007 Schones et al. 2008

  6. TF TF TF TF TF TF Transcriptional regulation by nucleosome and histone modification Nucleosome positioning is mainly repressive Histone modification can be either active or repressive H3K9ac Ace H3K27me3 TF target site

  7. Correlation between gene expression and different histone modification patterns Barski et al. 2007

  8. 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)

  9. 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

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

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