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

Details

Serval ID
serval:BIB_48096B19FD89
Type
Article: article from journal or magazin.
Collection
Publications
Title
Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions.
Journal
BMC genomics
Author(s)
Deforges J., Reis R.S., Jacquet P., Vuarambon D.J., Poirier Y.
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Publication state
Published
Issued date
22/07/2019
Peer-reviewed
Oui
Volume
20
Number
1
Pages
601
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
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 <sup>+</sup> and polysome-associated RNA of seedlings grown under high and low phosphate, or shoots and roots treated with different phytohormones, of which 550 were differentially regulated. Approximately 30% of lincRNAs showed conservation amongst Brassicaceae and 25% harbored transposon element (TE) sequences. Gene co-expression network analysis highlighted a group of lincRNAs associated with the response of roots to low phosphate. A total of 129 trans-NATs were predicted, of which 88 were significantly differentially expressed under at least one pairwise comparison. Five trans-NATs showed a positive correlation between their expression and target mRNA steady-state levels, and three showed a negative correlation. Expression of four trans-NATs positively correlated with a change in target mRNA polysome association. The regulatory potential of these trans-NATs did not implicate miRNA mimics nor siRNAs. We also looked for lincRNAs that could regulate gene expression in trans by Watson-Crick DNA:RNA base pairing with target protein-encoding loci. We identified 100 and 81 with a positive or negative correlation, respectively, with steady-state level of their predicted target. The regulatory potential of one such candidate lincRNA harboring a SINE TE sequence was validated in a protoplast assay on three distinct genes containing homologous TE sequence in their promoters. Construction of networks highlighted other putative lincRNAs with multiple predicted target loci for which expression was positively correlated with target gene expression.
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.
Keywords
Arabidopsis thaliana, Gene expression and regulation, Long intergenic non-coding RNA, Trans-natural antisense, Transposon
Pubmed
Open Access
Yes
Create date
04/08/2019 15:32
Last modification date
21/08/2019 6:37
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