DNAse Hyper-Sensitivity

BNFO 602 Biological Sequence Analysis, Spring 2014Mark Reimers, Ph.D

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 annealedFrom Western Kentucky U BioLab

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

~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

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

Where are DNAse Peaks?

From Thurman et al. Nature (2012)

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)

DNase I footprints mark sites of in vivo protein occupancy.

S Neph et al. Nature (2012)

S Neph et al. Nature (2012)

• Footprints are often highly conserved within DNAse peaks

DNAse I footprint patterns reflect transcription factor binding structures

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