1. DNAse Hyper-Sensitivity BNFO 602 Biological Sequence Analysis, Spring 2014 Mark Reimers, Ph.D

2. DNAse Hyper-sensitivity Two approaches: –Cut slowly then fragment and sequence ends –Cut rapidly then sequence short fragments DNAse I has distinctive base preferences Ragged double cuts must be annealed From Western Kentucky U BioLab

3. What DNAse-Seq Data Look Like Map reads to genome for cut points rather than overlaps –5’ end of + strand; 3’ end of minus strand Similar to ChIP-Seq with narrower peaks (mostly 150-200bp rather than ~300-400bp) Sample: Cerebrum from C57/B6 mice

4. ~100,000 – 250,000 DHSs per cell type (0.5-1.5% of genome) DNaseI Hypersensitive site (DHS) Promoters Enhancers DNaseI Hypersensitive Sites Mark Regulatory DNA in Diverse Samples Courtesy John Stamatoyannopoulos

5. What’s Under DNAse Peaks? Promoters, enhancers, insulators 98% of known regulatory sites are under DNAse peaks –Exceptions are mostly heterochromatin maintaining sites Splice regulatory sites typically not in DHS DHS do occur in exons

6. Where are DNAse Peaks? From Thurman et al. Nature (2012)

7. Digital Genomic Footprinting DNAse cannot easily cut at sites bound by proteins At very high read depths the ‘shadows’ cast by bound proteins show clearly S Neph et al. Nature (2012)

8. DNase I footprints mark sites of in vivo protein occupancy. S Neph et al. Nature (2012)

9. Footprints are often highly conserved within DNAse peaks DNAse I footprint patterns reflect transcription factor binding structures

10. Issue for DGF: DNaseI Sequence Biases DNaseI does not cut open DNA uniformly Patterns of peaks and valleys due to physical occlusion are confounded with sequence specificity due to DNA flexibility From Lazarovici et al PNAS 2013 DNase Sequence Cutting Biases