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Decoding Regulatory DNA Footprints for Transcriptome Analysis

Explore how DNase I footprints relate to transcription factor binding patterns, locate transcription start sites, and reveal novel regulatory elements. This study analyzes diverse cell and tissue types using billions of reads to decode an expansive cis-regulatory lexicon. Access raw and processed data at the provided links.

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Decoding Regulatory DNA Footprints for Transcriptome Analysis

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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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