title: Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes.
abstract: Histone mRNAs are rapidly degraded when DNA replication is inhibited during S phase with degradation initiating with oligouridylation of the stem loop at the 3' end. We developed a customized RNA sequencing strategy to identify the 3' termini of degradation intermediates of histone mRNAs. Using this strategy, we identified two types of oligouridylated degradation intermediates: RNAs ending at different sites of the 3' side of the stem loop that resulted from initial degradation by 3'hExo and intermediates near the stop codon and within the coding region. Sequencing of polyribosomal histone mRNAs revealed that degradation initiates and proceeds 3' to 5' on translating mRNA and that many intermediates are capped. Knockdown of the exosome-associated exonuclease PM/Scl-100, but not the Dis3L2 exonuclease, slows histone mRNA degradation consistent with 3' to 5' degradation by the exosome containing PM/Scl-100. Knockdown of No-go decay factors also slowed histone mRNA degradation, suggesting a role in removing ribosomes from partially degraded mRNAs.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Slevin
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Stacie
authors.initials: S
authors.lastname: Meaux
authors.affiliation: Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Welch
authors.affiliation: Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Bigler
authors.affiliation: Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Paula L
authors.initials: PL
authors.lastname: Miliani de Marval
authors.affiliation: Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Su
authors.affiliation: Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Rhoads
authors.affiliation: Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Jan F
authors.initials: JF
authors.lastname: Prins
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: marzluff@med.unc.edu.
authors.forename: William F
authors.initials: WF
authors.lastname: Marzluff
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D003062:Codon; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000235:genetics / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D006367:HeLa Cells; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D019169:Jurkat Cells; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D011132:Polyribosomes / Q000235:genetics* / Q000378:metabolism; D020871:RNA Stability; D016196:S Phase / Q000235:genetics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D014529:Uridine / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D003062:Codon; D006657:Histones; C571454:DIS3L2 protein, human; D005095:Exoribonucleases; D063326:Exosome Multienzyme Ribonuclease Complex; C077044:EXOSC10 protein, human; D014529:Uridine