title: Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs.
abstract: Mutations in the 3'-5' exonuclease DIS3L2 are associated with Perlman syndrome and hypersusceptibility to Wilms tumorigenesis. Previously, we found that Dis3l2 specifically recognizes and degrades uridylated pre-let-7 microRNA. However, the widespread relevance of Dis3l2-mediated decay of uridylated substrates remains unknown. Here, we applied an unbiased RNA immunoprecipitation strategy to identify Dis3l2 targets in mouse embryonic stem cells. The disease-associated long noncoding RNA (lncRNA) Rmrp, 7SL, as well as several other Pol III-transcribed noncoding RNAs (ncRNAs) were among the most highly enriched Dis3l2-bound RNAs. 3'-Uridylated Rmrp, 7SL, and small nuclear RNA (snRNA) species were highly stabilized in the cytoplasm of Dis3l2-depleted cells. Deep sequencing analysis of Rmrp 3' ends revealed extensive oligouridylation mainly on transcripts with imprecise ends. We implicate the terminal uridylyl transferases (TUTases) Zcchc6/11 in the uridylation of these ncRNAs, and biochemical reconstitution assays demonstrate the sufficiency of TUTase-Dis3l2 for Rmrp decay. This establishes Dis3l2-mediated decay (DMD) as a quality-control pathway that eliminates aberrant ncRNAs.
authors: Division of Hematology/Oncology, Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors: Mehdi
authors: M
authors: Pirouz
authors: Division of Hematology/Oncology, Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors: Peng
authors: P
authors: Du
authors: Division of Hematology/Oncology, Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.
authors: Marzia
authors: M
authors: Munafò
authors: Division of Hematology/Oncology, Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address: rgregory@enders.tch.harvard.edu.
authors: Richard I
authors: RI
authors: Gregory
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems; D002478:Cells, Cultured; D005095:Exoribonucleases / Q000172:deficiency / Q000235:genetics*; D000072669:Gene Editing; D005786:Gene Expression Regulation; D006801:Humans; D047468:Immunoprecipitation; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D011485:Protein Binding; D059367:RNA Cleavage; D012316:RNA Nucleotidyltransferases / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability; D020733:RNA, Small Cytoplasmic / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D018271:Signal Recognition Particle / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D014529:Uridine / Q000378:metabolism
chemical_list: C115990:7SL RNA; D035683:MicroRNAs; D020733:RNA, Small Cytoplasmic; D022661:RNA, Untranslated; D018271:Signal Recognition Particle; D012316:RNA Nucleotidyltransferases; C581306:Dis3l2 protein, mouse; D005095:Exoribonucleases; D014529:Uridine
keywords: 7SL; Dis3l2; Rmrp; TUTase; Zcchc11; Zcchc6; lncRNA; snRNA; uridylation