Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions.

Base Pairing Chromatin / genetics DNA Transposable Elements / genetics Gene Regulatory Networks Genetic Loci / genetics Promoter Regions, Genetic / genetics RNA, Antisense / genetics RNA, Long Noncoding / genetics
Arabidopsis thaliana Gene expression and regulation Long intergenic non-coding RNA Trans-natural antisense Transposon

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
22 Jul 2019
Historique:
received: 22 02 2019
accepted: 30 06 2019
entrez: 24 7 2019
pubmed: 25 7 2019
medline: 18 12 2019
Statut: epublish

Résumé

Long intergenic non-coding RNAs (lincRNAs) can act as regulators of expression of protein-coding genes. Trans-natural antisense transcripts (trans-NATs) are a type of lincRNAs that contain sequence complementary to mRNA from other loci. The regulatory potential of trans-NATs has been poorly studied in eukaryotes and no example of trans-NATs regulating gene expression in plants are reported. The goal of this study was to identify lincRNAs, and particularly trans-NATs, in Arabidopsis thaliana that have a potential to regulate expression of target genes in trans at the transcriptional or translational level. We identified 1001 lincRNAs using an RNAseq dataset from total polyA This study identified lincRNAs in Arabidopsis with potential in regulating target gene expression in trans by both RNA:RNA and RNA:DNA base pairing and highlights lincRNAs harboring TE sequences in such activity.

Sections du résumé

BACKGROUND BACKGROUND
Long intergenic non-coding RNAs (lincRNAs) can act as regulators of expression of protein-coding genes. Trans-natural antisense transcripts (trans-NATs) are a type of lincRNAs that contain sequence complementary to mRNA from other loci. The regulatory potential of trans-NATs has been poorly studied in eukaryotes and no example of trans-NATs regulating gene expression in plants are reported. The goal of this study was to identify lincRNAs, and particularly trans-NATs, in Arabidopsis thaliana that have a potential to regulate expression of target genes in trans at the transcriptional or translational level.
RESULTS RESULTS
We identified 1001 lincRNAs using an RNAseq dataset from total polyA
CONCLUSIONS CONCLUSIONS
This study identified lincRNAs in Arabidopsis with potential in regulating target gene expression in trans by both RNA:RNA and RNA:DNA base pairing and highlights lincRNAs harboring TE sequences in such activity.

Identifiants

DOI: 10.1186/s12864-019-5946-0 PMID: 31331261 PMC: PMC6647327
pubmed: 31331261
doi: 10.1186/s12864-019-5946-0
pii: 10.1186/s12864-019-5946-0
pmc: PMC6647327
doi:

Substances chimiques

Chromatin 0
DNA Transposable Elements 0
RNA, Antisense 0
RNA, Long Noncoding 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

601

Subventions

Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)
ID : 31003A_159998
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
ID : CRSII3_154471

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Auteurs

Jules Deforges (J)

Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.

Rodrigo S Reis (RS)

Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.

Philippe Jacquet (P)

Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.

Dominique Jacques Vuarambon (DJ)

Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.

Yves Poirier (Y)

Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland. yves.poirier@unil.ch.
ORCID: 0000-0001-8660-294X

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Appariement de bases › Prediction of regulatory long intergenic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Prediction of regulatory long intergenic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Éléments transposables d'ADN › Prediction of regulatory long intergenic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › Réseaux de régulation génique › Prediction of regulatory long intergenic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Locus génétiques › Prediction of regulatory long intergenic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Éléments de régulation transcriptionnelle › Régions promotrices (génétique) › Prediction of regulatory long intergenic...
questionsmedicales.fr › Actions chimiques et utilisations › Utilisations spécialisées de produits chimiques › Produits chimiques de laboratoire › Sondes moléculaires › Sondes d'acide nucléique › Éléments antisens (génétique) › ARN antisens › Prediction of regulatory long intergenic...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › ARN long non codant › Prediction of regulatory long intergenic...