Download - Chao He 2012-09-19
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Chao He2012-09-19
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Outline
• Data Summary and Sources
• Analysis of Footprints
• Summary
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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
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footprints: DNA segments protected by proteins that are not sensitivity to DNase I enzyme
Regulatory DNA is populated with DNase I footprints
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Footprints are quantitative markers of factor occupancy
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Footprints harbour functional SNVs and lack methylation
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Transcription factor structure is imprinted on the genome
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A 50-bp footprint localizes transcription initiation
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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
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Footprints encode an expansive cis-regulatory lexicon
ji
ijji pp,
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Novel motif occupancy parallels regulators of cell fate
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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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Thank you