Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana.
The biological relevance of long non-coding RNAs (lncRNAs) is emerging. Whether the lncRNAs could form structured precursors for small RNAs (sRNAs) production remains elusive. Here, 172 713 DCL1 (Dicer-like 1)-dependent sRNAs were identified in Arabidopsis. Except for the sRNAs mapped onto the microRNA precursors, the remaining ones led us to investigate their originations. Intriguingly, 65 006 sRNAs found their loci on 5891 lncRNAs. These sRNAs were sent to AGO (Argonaute) enrichment analysis. As a result, 1264 sRNAs were enriched in AGO1, which were then subjected to target prediction. Based on degradome sequencing data, 109 transcripts were validated to be targeted by 96 sRNAs. Besides, 44 lncRNAs were targeted by 23 sRNAs. To further support the origination of the DCL1-dependent sRNAs from lncRNAs, we searched for the degradome-based cleavage signals at either ends of the sRNA loci, which were supposed to be produced during DCL1-mediated processing of the long-stem structures. As a result, 63 612 loci were supported by degradome signatures. Among these loci, 6606 reside within the dsRNA-seq (double-stranded RNA sequencing) read-covered regions of 100 nt or longer. These regions were subjected to secondary structure prediction. And, 43 regions were identified to be capable of forming highly complementary long-stem structures. We proposed that these local long-stem structures could be recognized by DCL1 for cropping, thus serving as the sRNA precursors. We hope that our study could inspire more research efforts to study on the biological roles of the lncRNAs in plants.
College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, P.R. China.
Xiaoxia
X
Ma
College of Life Sciences; Huzhou Teachers College; Huzhou, P.R. China.
Chaogang
C
Shao
Institute of Biochemistry; College of Life Sciences; Zhejiang University; Hangzhou, P.R. China.
Yongfeng
Y
Jin
College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, P.R. China.
Huizhong
H
Wang
College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, P.R. China.
Yijun
Y
Meng
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D060565:Argonaute Proteins / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000235:genetics; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism
D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D018797:Cell Cycle Proteins; D035683:MicroRNAs; D012330:RNA, Double-Stranded; D062085:RNA, Long Noncoding; C402383:DCL1 protein, Arabidopsis; D043244:Ribonuclease III
AGO (Argonaute); Arabidopsis thaliana; DCL1 (Dicer-like 1); degradome; dsRNA-seq (double-stranded RNA sequencing); lncRNA (long non-coding RNA); sRNA (small RNA)