title: DNase footprint signatures are dictated by factor dynamics and DNA sequence.
abstract: Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a timescale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor-binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach.
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
authors.forename: Myong-Hee
authors.initials: MH
authors.lastname: Sung
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Guertin
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
authors.forename: Songjoon
authors.initials: S
authors.lastname: Baek
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA. Electronic address: hagerg@exchange.nih.gov.
authors.forename: Gordon L
authors.initials: GL
authors.lastname: Hager
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D053837:DNA Cleavage; D018983:DNA Footprinting; D003850:Deoxyribonuclease I / Q000737:chemistry; D004706:Endodeoxyribonucleases / Q000737:chemistry; D023281:Genomics; D006801:Humans; D011485:Protein Binding / Q000235:genetics; D017434:Protein Structure, Tertiary; D012372:ROC Curve; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA; D004706:Endodeoxyribonucleases; D003850:Deoxyribonuclease I; C019329:deoxyribonuclease II