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Int. J. Mol. Sci. 2015, 16(6), 13937-13958; doi:10.3390/ijms160613937

Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing

1,2,3,†
,
1,2,3,†
,
1,2,3
and
1,2,3,*
1
National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
2
Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China
3
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Ann Cuypers
Received: 17 April 2015 / Revised: 21 May 2015 / Accepted: 1 June 2015 / Published: 18 June 2015
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
View Full-Text   |   Download PDF [1112 KB, uploaded 18 June 2015]   |  

Abstract

miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. View Full-Text
Keywords: degradome; miRNA; miRNA*; precursor; targets; Populus tomentosa degradome; miRNA; miRNA*; precursor; targets; Populus tomentosa
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Chen, M.; Bao, H.; Wu, Q.; Wang, Y. Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing. Int. J. Mol. Sci. 2015, 16, 13937-13958.

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