DNAse Hyper-Sensitivity
description
Transcript of DNAse Hyper-Sensitivity
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