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Chao He 2012-09-19

Chao He 2012-09-19. Outline. Data Summary and Sources Analysis of Footprints Summary. Data. 41 diverse cell and tissue types 14.9 billion reads, 11.2 billion unique reads ~273 million reads / cell-type Raw Data: GSE26328 and GSE18927

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Chao He 2012-09-19

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  1. Chao He 2012-09-19

  2. Outline • Data Summary and Sources • Analysis of Footprints • Summary

  3. Data • 41 diverse cell and tissue types 14.9 billion reads, 11.2 billion unique reads ~273 million reads / cell-type • Raw Data: GSE26328 and GSE18927 • Processed data: ftp://ftpprivate.ebi.ac.uk/ Login:encode-box-01 Password:enc*deDOWN

  4. Regulatory DNA is populated with DNase I footprints footprints: DNA segments protected by proteins that are not sensitivity to DNase I enzyme

  5. Footprints are quantitative markers of factor occupancy

  6. Footprints harbour functional SNVs and lack methylation

  7. Transcription factor structure is imprinted on the genome

  8. A 50-bp footprint localizes transcription initiation

  9. Distinguishing indirect transcription factor occupancy Directly bound sites: ChIP-seq peaks containing a compatible footprinted motif Indirectly bound sites : ChIP-seq peaks lacking a compatible motif or footprint Colour of each cell: indirect peaks that co-localize with the direct peaks of another factor

  10. Footprints encode an expansive cis-regulatory lexicon

  11. Novel motif occupancy parallels regulators of cell fate

  12. Summary • DNase I footprints are importantly related to TFs’ binding pattern and intensity • A 50-bp footprint help to locate TSS • Footprints can recovery TF’s motif and identify novel regulatory element

  13. Thank you

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