title: RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells.
abstract: The histone chaperone HIRA is involved in depositing histone variant H3.3 into distinct genic regions, including promoters, enhancers, and gene bodies. However, how HIRA deposits H3.3 to these regions remains elusive. Through a short hairpin RNA (shRNA) screening, we identified single-stranded DNA binding protein replication protein A (RPA) as a regulator of the deposition of newly synthesized H3.3 into chromatin. We show that RPA physically interacts with HIRA to form RPA-HIRA-H3.3 complexes, and it co-localizes with HIRA and H3.3 at gene promoters and enhancers. Depletion of RPA1, the largest subunit of the RPA complex, dramatically reduces both HIRA association with chromatin and the deposition of newly synthesized H3.3 at promoters and enhancers and leads to altered transcription at gene promoters. These results support a model whereby RPA, best known for its role in DNA replication and repair, recruits HIRA to promoters and enhancers and regulates deposition of newly synthesized H3.3 to these regulatory elements for gene regulation.
authors.affiliation: Departments of Pediatrics and Genetics and Development, Institute for Cancer Genetics, Irving Cancer Research Center, College of Surgeons and Physicians, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
authors.forename: Honglian
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Departments of Pediatrics and Genetics and Development, Institute for Cancer Genetics, Irving Cancer Research Center, College of Surgeons and Physicians, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
authors.forename: Haiyun
authors.initials: H
authors.lastname: Gan
authors.affiliation: Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Zhiquan
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Jeong-Heon
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Departments of Pediatrics and Genetics and Development, Institute for Cancer Genetics, Irving Cancer Research Center, College of Surgeons and Physicians, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Tamas
authors.initials: T
authors.lastname: Ordog
authors.affiliation: Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Marc S
authors.initials: MS
authors.lastname: Wold
authors.affiliation: Departments of Radiation Oncology and Environmental Health Sciences, Translational Oncology Program and Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Mats
authors.initials: M
authors.lastname: Ljungman
authors.affiliation: Departments of Pediatrics and Genetics and Development, Institute for Cancer Genetics, Irving Cancer Research Center, College of Surgeons and Physicians, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA. Electronic address: zz2401@cumc.columbia.edu.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D001665:Binding Sites; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D016193:G1 Phase; D057809:HEK293 Cells; D006367:HeLa Cells; D056488:Histone Chaperones / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D034622:RNA Interference; D051716:Replication Protein A / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D018797:Cell Cycle Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; C086057:HIRA protein, human; D056488:Histone Chaperones; D006657:Histones; C497167:RPA1 protein, human; C534779:RPA3 protein, human; D051716:Replication Protein A; D014157:Transcription Factors; D004247:DNA; C516794:RPA2 protein, human
keywords: H3.3 deposition; HIRA; R-loop; RPA; enhancer; histone chaperone; nucleosome assembly; promoter