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Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response.
- Source :
-
BMC Genomics . 11/15/2019, Vol. 20 Issue 1, p1-17. 17p. 1 Diagram, 3 Charts, 5 Graphs. - Publication Year :
- 2019
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Abstract
- Background: Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results: We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions: Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 20
- Issue :
- 1
- Database :
- Academic Search Index
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- 139690488
- Full Text :
- https://doi.org/10.1186/s12864-019-6245-5