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 Processed data: ftp://ftpprivate.ebi.ac.uk/ Login:encode-box-01 Password:enc*deDOWN

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

Footprints are quantitative markers of factor occupancy

Footprints harbour functional SNVs and lack methylation

Transcription factor structure is imprinted on the genome

A 50-bp footprint localizes transcription initiation

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

Footprints encode an expansive cis-regulatory lexicon

Novel motif occupancy parallels regulators of cell fate

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

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