DNAse Hyper-Sensitivity

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. DNaseIHypersensitive Sites Mark Regulatory DNA in Diverse Samples Promoters DNaseI Hypersensitive site (DHS) Enhancers ~100,000 – 250,000 DHSs per cell type (0.5-1.5% of genome) 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 Nephet al. Nature(2012)

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

9. DNAse I footprint patterns reflect transcription factor binding structures • Footprints are often highly conserved within DNAse peaks S Nephet al. Nature(2012)

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 DNase Sequence Cutting Biases From Lazarovici et al PNAS 2013