Chao He2012-09-19

Outline

• Data Summary and Sources

• Analysis of Footprints

• Summary

Data

• 41 diverse cell and tissue types14.9 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

footprints: DNA segments protected by proteins that are not sensitivity to DNase I enzyme

Regulatory DNA is populated with DNase I footprints

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 acompatible footprinted motif

Indirectly bound sites :ChIP-seq peakslacking 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

ji

ijji pp,

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

Thank you