TY - JOUR
T1 - Identification of cold-inducible microRNAs in plants by transcriptome analysis
AU - Zhou, Xuefeng
AU - Wang, Guandong
AU - Sutoh, Keita
AU - Zhu, Jian Kang
AU - Zhang, Weixiong
N1 - Funding Information:
This research was supported in part by NSF grants ITR/EIA-0113618 and IIS-0535257 and a grant from Monsanto Corporation to WZ, and by a NSF grant to JKZ.
PY - 2008/11
Y1 - 2008/11
N2 - MicroRNAs are ~ 21-nt long, non-coding RNAs that play critical roles in post-transcriptional gene regulation. Even though a large number of miRNAs have been identified, annotating their functions remains a challenge. We develop a computational, transcriptome-based approach to annotating stress-inducible microRNAs in plants. With this approach, we find that nineteen microRNA genes of eleven microRNA families in Arabidopsis thaliana are up-regulated by cold stress. Our experiments validate that among the eleven microRNAs, eight are differentially induced and three are constantly expressed under low temperature. Our result expands the number of cold-inducible microRNAs from four to eight. A promoter analysis further reveals that the cold-responsive microRNA genes contain many known stress-related cis-regulatory elements in their promoters. Our analysis also indicates that many signaling pathways, such as auxin pathways, may be affected by cold-inducible microRNAs. Our approach can be applied to plant microRNAs responding to other abiotic and biotic stresses. The research demonstrates that machine learning methods, augmented by wet-lab analysis, hold a great promise for functional annotation of microRNAs.
AB - MicroRNAs are ~ 21-nt long, non-coding RNAs that play critical roles in post-transcriptional gene regulation. Even though a large number of miRNAs have been identified, annotating their functions remains a challenge. We develop a computational, transcriptome-based approach to annotating stress-inducible microRNAs in plants. With this approach, we find that nineteen microRNA genes of eleven microRNA families in Arabidopsis thaliana are up-regulated by cold stress. Our experiments validate that among the eleven microRNAs, eight are differentially induced and three are constantly expressed under low temperature. Our result expands the number of cold-inducible microRNAs from four to eight. A promoter analysis further reveals that the cold-responsive microRNA genes contain many known stress-related cis-regulatory elements in their promoters. Our analysis also indicates that many signaling pathways, such as auxin pathways, may be affected by cold-inducible microRNAs. Our approach can be applied to plant microRNAs responding to other abiotic and biotic stresses. The research demonstrates that machine learning methods, augmented by wet-lab analysis, hold a great promise for functional annotation of microRNAs.
KW - MicroRNAs
KW - Post-transcriptional regulation
KW - Stress response
KW - Transcriptome modeling
KW - cis-elements
UR - http://www.scopus.com/inward/record.url?scp=55049118172&partnerID=8YFLogxK
U2 - 10.1016/j.bbagrm.2008.04.005
DO - 10.1016/j.bbagrm.2008.04.005
M3 - Article
C2 - 18471443
AN - SCOPUS:55049118172
SN - 1874-9399
VL - 1779
SP - 780
EP - 788
JO - Biochimica et Biophysica Acta - Gene Regulatory Mechanisms
JF - Biochimica et Biophysica Acta - Gene Regulatory Mechanisms
IS - 11
ER -