Profiling of cold-stress-responsive miRNAs in rice by microarrays

• Published in: Gene Vol. 459; no. 1; pp. 39 - 47
• Main Authors: Lv, De-Kang, Bai, Xi, Li, Yong, Ding, Xiao-Dong, Ge, Ying, Cai, Hua, Ji, Wei, Wu, Nalahu, Zhu, Yan-Ming
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2010
• Subjects: Base Sequence; Biomarkers - metabolism; Cold stress; Cold Temperature; DNA microarrays; Gene Expression Profiling; Gene Expression Regulation, Plant; Microarray; MicroRNA; MicroRNAs - physiology; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Oryza - genetics; Oryza - growth & development; Oryza - metabolism; Oryza sativa; Regulatory Sequences, Nucleic Acid; Sequence Homology, Nucleic Acid; LTI; ABA; RISC; TEs; miRNAs; COR; AGO; ABRE; MeJA; LTR; GARE; Microarray; SA; KIN; Oryza sativa; RD; MicroRNA; Cold stress; ARE; TSS; GA3; DCL1; HSE; MBS
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2010.03.011

MicroRNAs (miRNAs) are small single-stranded RNAs with a length of about 21 nt; these non-coding RNAs regulate developmental and stress responses in plants by cleaving mRNAs. Cold stress is one of the most severe abiotic stresses and adversely affects rice yields by restraining sowing time, causing tissue damage, and stunting growth. Although many miRNAs have been identified in rice, little is known about the role of miRNAs in the response to cold stress. In this study, we identified 18 cold-responsive rice miRNAs using microarrays. Most were down-regulated. Members of the miR-167 and miR-319 families showed similar profiles. Intriguingly, members of miR-171 family showed diverse expression patterns. Three miRNAs derived from transposable element sequence were clustered within an intron and proved to be co-transcribed with the host gene only under cold stress. The existence of hormone-responsive elements in the upstream regions of the cold-responsive miRNAs indicates the importance of hormones in this defense system mediated by miRNAs. Two miRNA target pairs validated by 5′ RACE showed opposite expression profiles under cold stress. Finally, the predicted stress-related targets of these miRNAs provided further evidence supporting our results. These findings confirm the role of miRNAs as ubiquitous regulators in rice.