Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

• Published in: BMC genomics Vol. 20; no. 1; pp. 864 - 17
• Main Authors: Lv, Yuanda, Hu, Fengqin, Zhou, Yongfeng, Wu, Feilong, Gaut, Brandon S.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 15.11.2019; BioMed Central; BMC
• Subjects: Abiotic stress; Adaptation, Physiological - genetics; Co-expression network; Cold Temperature; Corn; DNA; DNA Transposable Elements; Droughts; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes; Genome, Plant; Genomics; Hot Temperature; Long non-coding RNA; RNA; RNA sequencing; RNA, Long Noncoding - classification; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Plant - classification; RNA, Plant - genetics; RNA, Plant - metabolism; Salinity; Sequence Analysis, RNA; Stress, Physiological - genetics; Transposable elements; Transposons; Zea mays - genetics; Zea mays - metabolism; Abiotic stress; Co-expression network; Transposable elements; Long non-coding RNA
• DOI: 10.1186/s12864-019-6245-5
• ISSN: 1471-2164

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. 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. 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.