title: RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription.
abstract: We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using chromatin immunoprecipitation sequencing (ChIP-seq) versus TOP1 activity using topoisomerase 1 sequencing (TOP1-seq), a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. TOP1 stimulation is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release. Thus the coordinated action of BRD4 and TOP1 overcame the torsional stress opposing transcription as RNAPII commenced elongation but preserved negative supercoiling that assists promoter melting at start sites. This nexus between transcription and DNA topology promises to elicit new strategies to intercept pathological gene expression.
authors.affiliation: Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Baranello
authors.affiliation: Computational Biology Branch, NCBI/NIH, Bethesda, MD 20892, USA.
authors.forename: Damian
authors.initials: D
authors.lastname: Wojtowicz
authors.affiliation: Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA.
authors.forename: Kairong
authors.initials: K
authors.lastname: Cui
authors.affiliation: Experimental Immunology Branch, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Ballachanda N
authors.initials: BN
authors.lastname: Devaiah
authors.affiliation: Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Hye-Jung
authors.initials: HJ
authors.lastname: Chung
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Ka Yim
authors.initials: KY
authors.lastname: Chan-Salis
authors.affiliation: Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA.
authors.forename: Rajarshi
authors.initials: R
authors.lastname: Guha
authors.affiliation: Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA.
authors.forename: Kelli
authors.initials: K
authors.lastname: Wilson
authors.affiliation: Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA.
authors.forename: Xiaohu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Lymphoid Malignancies Branch, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Piotrowski
authors.affiliation: Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA.
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Thomas
authors.affiliation: Experimental Immunology Branch, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Dinah S
authors.initials: DS
authors.lastname: Singer
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
authors.affiliation: Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Yves
authors.initials: Y
authors.lastname: Pommier
authors.affiliation: Computational Biology Branch, NCBI/NIH, Bethesda, MD 20892, USA.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Przytycka
authors.affiliation: Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kouzine
authors.affiliation: Lymphoid Malignancies Branch, NCI/NIH, Bethesda, MD 20892, USA.
authors.forename: Brian A
authors.initials: BA
authors.lastname: Lewis
authors.affiliation: Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA. Electronic address: zhaok@nhlbi.nih.gov.
authors.forename: Keji
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA. Electronic address: levens@helix.nih.gov.
authors.forename: David
authors.initials: D
authors.lastname: Levens
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004264:DNA Topoisomerases, Type I / Q000235:genetics / Q000378:metabolism*; D055785:Gene Knockdown Techniques; D006801:Humans; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D061805:Transcription Elongation, Genetic; D014157:Transcription Factors / Q000302:isolation & purification; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors; D004247:DNA; D012319:RNA Polymerase II; D004264:DNA Topoisomerases, Type I; C528909:TOP1 protein, human