Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Abstract

Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

“…Many studies have reported that APA is highly involved in external environmental responses in plants (Shen et al ., ; Thomas et al ., ; de Lorenzo et al ., ; Hong et al ., ), for example the generation of more non‐canonical APA sites under hypoxia stress in Arabidopsis (de Lorenzo et al ., ). In rice, the reduction of core poly(A) factors such as CstF77, ESP1, CPSF100 and CPSF73 suppresses the polyadenylation of long non‐coding RNAs in response to drought and salt stress (Yuan et al ., ). Our results indicated that subspecies‐specific usage of APA sites largely contributed to the differential stress and defense tolerance of indica and japonica (Figure ).…”

Transposable elements contribute to regulatory hub stress-related long noncoding RNAs in Maize

“…However, lncRNAs can also be non-polyadenylated, and hence robust lncRNA discovery requires consideration of both polyadenylated and non-polyadenylated RNA samples. The second is that lncRNAs tend to be expressed at lower levels than coding genes, but with pre cis e spatio-temporal patterns [3, 7–13]. A third general property is that some lncRNAs overlap with coding regions and sometimes contain parts of an exon; however, most originate from intergenic spaces (and these are sometimes called long intergenic RNAs or lincRNAs).…”

“…The expression of 28% (1,832 of 6,480) of Arabidopsis lncRNAs was found to be significantly altered under biotic and/or abiotic stresses [4]. These findings – i.e., that lncRNAs are associated with stress responses – are particularly important in the context of crop species, because abiotic stresses affect crop yield and quality [13, 25–29]. However, the identification of lncRNAs during crop stress response remains largely unexplored, with a few notable exceptions.…”

Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed

“…For example, circRNAs may be involved in chilling injury in tomato (Zuo et al, 2016), or may respond to imbalances in iron and zinc (Darbani et al, 2016). Similar results were reported for another circRNA derived from the phytoene desaturase gene (Tan et al, 2017). This was likely due to the continuous highly expressed circRNA and/or the low abundance of linear RNA from the overexpression vector.…”