Imperial College London
Dr Samuel Marguerat

DrSamuelMarguerat

Faculty of Natural Sciences, Department of Mathematics

Visiting Researcher
 
 
 
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Contact

 

+44 (0)20 3313 8331samuel.marguerat Website

 
 
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Location

 

5003CRB (Clinical Research Building)Hammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Atkinson:2018:10.1261/rna.065524.118,
author = {Atkinson, S and Marguerat, S and Bitton, D and Bachand, F and Rodriguez-Lopez, M and Rallis, C and Lemay, J-F and Cotobal, C and Malecki, M and Smialowski, P and Mata, J and Korber, P and Bahler, J},
doi = {10.1261/rna.065524.118},
journal = {RNA},
pages = {1195--1213},
title = {Long non-coding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast},
url = {http://dx.doi.org/10.1261/rna.065524.118},
volume = {24},
year = {2018}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive non-coding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyse 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-times 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.
AU  - Atkinson,S
AU  - Marguerat,S
AU  - Bitton,D
AU  - Bachand,F
AU  - Rodriguez-Lopez,M
AU  - Rallis,C
AU  - Lemay,J-F
AU  - Cotobal,C
AU  - Malecki,M
AU  - Smialowski,P
AU  - Mata,J
AU  - Korber,P
AU  - Bahler,J
DO  - 10.1261/rna.065524.118
EP  - 1213
PY  - 2018///
SN  - 1355-8382
SP  - 1195
TI  - Long non-coding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast
T2  - RNA
UR  - http://dx.doi.org/10.1261/rna.065524.118
UR  - https://www.ncbi.nlm.nih.gov/pubmed/29914874
UR  - http://hdl.handle.net/10044/1/61490
VL  - 24
ER  -
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