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Characterization of stress‐responsive lnc RNA s in A rabidopsis thaliana by integrating expression, epigenetic and structural features
Author(s) -
Di Chao,
Yuan Jiapei,
Wu Yue,
Li Jingrui,
Lin Huixin,
Hu Long,
Zhang Ting,
Qi Yijun,
Gerstein Mark B.,
Guo Yan,
Lu Zhi John
Publication year - 2014
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12679
Subject(s) - rna , biology , non coding rna , gene expression , rna binding protein , microbiology and biotechnology , gene , genetics , epigenetics , transcription (linguistics) , computational biology , linguistics , philosophy
Summary Recently, in addition to poly(A)+ long non‐coding RNA s (lnc RNA s), many lnc RNA s without poly(A) tails, have been characterized in mammals. However, the non‐polyA lnc RNA s and their conserved motifs, especially those associated with environmental stresses, have not been fully investigated in plant genomes. We performed poly(A)− RNA ‐seq for seedlings of A rabidopsis thaliana under four stress conditions, and predicted lnc RNA transcripts. We classified the lnc RNA s into three confidence levels according to their expression patterns, epigenetic signatures and RNA secondary structures. Then, we further classified the lnc RNA s to poly(A)+ and poly(A)− transcripts. Compared with poly(A)+ lncRNAs and coding genes, we found that poly(A)− lncRNAs tend to have shorter transcripts and lower expression levels, and they show significant expression specificity in response to stresses. In addition, their differential expression is significantly enriched in drought condition and depleted in heat condition. Overall, we identified 245 poly(A)+ and 58 poly(A)− lnc RNA s that are differentially expressed under various stress stimuli. The differential expression was validated by q RT ‐ PCR , and the signaling pathways involved were supported by specific binding of transcription factors ( TF s), phytochrome‐interacting factor 4 ( PIF 4) and PIF 5. Moreover, we found many conserved sequence and structural motifs of lnc RNA s from different functional groups (e.g. a UUC motif responding to salt and a AU‐rich stem‐loop responding to cold), indicated that the conserved elements might be responsible for the stress‐responsive functions of lnc RNA s.