PuSH - Publikationsserver des Helmholtz Zentrums München

Atkinson, S.R.* ; Marguerat, S.* ; Bitton, D.A.* ; Rodriguez-Lopez, M.* ; Rallis, C.* ; Lemay, J.* ; Cotobal, C.* ; Malecki, M.* ; Smialowski, P. ; Mata, J.* ; Korber, P.* ; Bachand, F.* ; Bahler, J.*

Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast.

RNA 24, 1195-1213 (2018)
Verlagsversion DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
Altmetric
Weitere Metriken?
[➜Einloggen]
Zusatzinfos bearbeiten [➜Einloggen]
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Antisense Rna ; Cytoplasmic Exonuclease ; Nmd Pathway ; Pervasive Transcription ; Rna Degradation ; Schizosaccharomyces Pombe; Schizosaccharomyces-pombe Genome; Gene-expression; Messenger-rnas; Transcription Termination; Saccharomyces-cerevisiae; Pervasive Transcription; Poly(a)-binding Protein; Antisense Transcription; Polymerase-ii; S. Pombe
ISSN (print) / ISBN 1355-8382
e-ISSN 1469-9001
Zeitschrift RNA
Quellenangaben Band: 24, Heft: 9, Seiten: 1195-1213 Artikelnummer: , Supplement: ,
Verlag Cold Spring Harbor Laboratory Press
Verlagsort 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Stem Cell Research (ISF)