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DNase-capture reveals differential transcription factor binding modalities.

ABSTRACT: We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites.

SUBMITTER: Kang D

PROVIDER: S-EPMC5746236 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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DNase-capture reveals differential transcription factor binding modalities.

Kang Daniel D Sherwood Richard R Barkal Amira A Hashimoto Tatsunori T Engstrom Logan L Gifford David D

PloS one 20171228 12

We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites. ...[more]

PMID: 29284001

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