title: Nucleosomes accelerate transcription factor dissociation.
abstract: Transcription factors (TF) bind DNA-target sites within promoters to activate gene expression. TFs target their DNA-recognition sequences with high specificity by binding with resident times of up to hours in vitro. However, in vivo TFs can exchange on the order of seconds. The factors that regulate TF dynamics in vivo and increase dissociation rates by orders of magnitude are not known. We investigated TF binding and dissociation dynamics at their recognition sequence within duplex DNA, single nucleosomes and short nucleosome arrays with single molecule total internal reflection fluorescence (smTIRF) microscopy. We find that the rate of TF dissociation from its site within either nucleosomes or nucleosome arrays is increased by 1000-fold relative to duplex DNA. Our results suggest that TF binding within chromatin could be responsible for the dramatic increase in TF exchange in vivo. Furthermore, these studies demonstrate that nucleosomes regulate DNA-protein interactions not only by preventing DNA-protein binding but by dramatically increasing the dissociation rate of protein complexes from their DNA-binding sites.
authors.affiliation: Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Luo
authors.forename: Justin A
authors.initials: JA
authors.lastname: North
authors.forename: Sean D
authors.initials: SD
authors.lastname: Rose
authors.forename: Michael G
authors.initials: MG
authors.lastname: Poirier
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D004247:DNA / Q000378:metabolism; D007700:Kinetics; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D012697:Serine Endopeptidases / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D000099160:LexA Repressor Protein
chemical_list: D001426:Bacterial Proteins; D004247:DNA; D009707:Nucleosomes; D012697:Serine Endopeptidases; D014157:Transcription Factors; D000099160:LexA Repressor Protein