1. Chao He

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