title: Dynamic regulation of transcription factors by nucleosome remodeling.
abstract: The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States.
authors.forename: Arjan
authors.initials: A
authors.lastname: Hada
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States.
authors.forename: Payel
authors.initials: P
authors.lastname: Sen
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States.
authors.forename: Lola
authors.initials: L
authors.lastname: Olufemi
authors.affiliation: Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Hall
authors.affiliation: Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States.
authors.forename: Benjamin Y
authors.initials: BY
authors.lastname: Smith
authors.affiliation: Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States.
authors.forename: Scott
authors.initials: S
authors.lastname: Forth
authors.affiliation: Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.
authors.forename: Jeffrey N
authors.initials: JN
authors.lastname: McKnight
authors.affiliation: Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.
authors.forename: Ashok
authors.initials: A
authors.lastname: Patel
authors.affiliation: Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Bowman
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States.
authors.forename: Blaine
authors.initials: B
authors.lastname: Bartholomew
authors.affiliation: Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States.
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Wang
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism*; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008954:Models, Biological; D009707:Nucleosomes / Q000502:physiology*; D052898:Optical Tweezers; D010957:Plasmids / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D009707:Nucleosomes; C445179:SWI-SNF-B chromatin-remodeling complex; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA; D000251:Adenosine Triphosphatases; C470546:ISW1 protein, S cerevisiae
keywords: S. cerevisiae; biochemistry; biophysics; chromatin remodeling; gene regulation; optical trapping; single molecule studies; structural biology; transcription factor