title: The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3' ends.
abstract: Herpesvirus saimiri (HVS) is an oncogenic γ-herpesvirus that produces microRNAs (miRNAs) by cotranscription of precursor miRNA (pre-miRNA) hairpins immediately downstream from viral small nuclear RNAs (snRNA). The host cell Integrator complex, which recognizes the snRNA 3' end processing signal (3' box), generates the 5' ends of HVS pre-miRNA hairpins. Here, we identify a novel 3' box-like sequence (miRNA 3' box) downstream from HVS pre-miRNAs that is essential for miRNA biogenesis. In vivo knockdown and rescue experiments confirmed that the 3' end processing of HVS pre-miRNAs also depends on Integrator activity. Interaction between Integrator and HVS primary miRNA (pri-miRNA) substrates that contain only the miRNA 3' box was confirmed by coimmunoprecipitation and an in situ proximity ligation assay (PLA) that we developed to localize specific transient RNA-protein interactions inside cells. Surprisingly, in contrast to snRNA 3' end processing, HVS pre-miRNA 3' end processing by Integrator can be uncoupled from transcription, enabling new approaches to study Integrator enzymology.
authors.affiliation: Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA;
authors.forename: Mingyi
authors.initials: M
authors.lastname: Xie
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA;
authors.forename: Mei-Di
authors.initials: MD
authors.lastname: Shu
authors.affiliation: Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA;
authors.forename: Acer
authors.initials: A
authors.lastname: Xu
authors.affiliation: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA.
authors.forename: Diana A
authors.initials: DA
authors.lastname: Lenis
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
authors.forename: Daniel
authors.initials: D
authors.lastname: DiMaio
authors.affiliation: Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA;
authors.forename: Joan A
authors.initials: JA
authors.lastname: Steitz
mesh_terms: D055785:Gene Knockdown Techniques; D057809:HEK293 Cells; D006367:HeLa Cells; D006567:Herpesvirus 2, Saimiriine / Q000235:genetics* / Q000378:metabolism; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D046912:Multiprotein Complexes / Q000235:genetics / Q000378:metabolism; D026721:RNA 3' End Processing / Q000235:genetics / Q000502:physiology*; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D046912:Multiprotein Complexes; D012322:RNA Precursors; D012342:RNA, Small Nuclear
keywords: Herpesvirus saimiri; Integrator; microRNA biogenesis; proximity ligation assay; snRNA 3′ end processing