Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

Nat Methods. 2014 Jan;11(1):73-78. doi: 10.1038/nmeth.2762. Epub 2013 Dec 8.


Sequencing of DNase I hypersensitive sites (DNase-seq) is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize performance of DNase-seq. Sequencing short fragments of 50-100 base pairs (bp) that accumulate in long internucleosome linker regions was more efficient for identifying transcription factor binding sites compared to sequencing longer fragments. We also assessed the potential of DNase-seq to predict transcription factor occupancy via generation of nucleotide-resolution transcription factor footprints. In modeling the sequence-specific DNase I cutting bias, we found a strong effect that varied over more than two orders of magnitude. This indicates that the nucleotide-resolution cleavage patterns at many transcription factor binding sites are derived from intrinsic DNase I cleavage bias rather than from specific protein-DNA interactions. In contrast, quantitative comparison of DNase I hypersensitivity between states can predict transcription factor occupancy associated with particular biological perturbations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Cell Line, Tumor
  • Chromatin / chemistry
  • Deoxyribonuclease I / chemistry*
  • Female
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Humans
  • K562 Cells
  • MCF-7 Cells
  • Male
  • Nucleosomes / chemistry
  • Nucleotides / chemistry
  • Receptors, Androgen / chemistry
  • Sequence Analysis, DNA / methods*
  • Transcription Factors / chemistry*
  • Tumor Suppressor Protein p53 / chemistry


  • Chromatin
  • Nucleosomes
  • Nucleotides
  • Receptors, Androgen
  • TP53 protein, human
  • Transcription Factors
  • Tumor Suppressor Protein p53
  • Deoxyribonuclease I

Associated data

  • GEO/GSE51915