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. 2012 Jul;63(12):4597-613.
doi: 10.1093/jxb/ers136. Epub 2012 Jul 3.

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

Zhao Sheng Zhou  1 , Jian Bo Song, Zhi Min Yang
Affiliations

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

Zhao Sheng Zhou et al. J Exp Bot. 2012 Jul.

Abstract

MicroRNAs (miRNAs) are a distinct class of small RNAs in plants that not only regulate biological processes but also regulate response to environmental stresses. The toxic heavy metal cadmium (Cd) induces expression of several miRNAs in rapeseed (Brassica napus), but it is not known on a genome-wide scale how the expression of miRNAs and their target genes, is regulated by Cd. In this study, four small RNA libraries and four degradome libraries were constructed from Cd-treated and non-Cd-treated roots and shoots of B. napus seedlings. Using high-throughput sequencing, the study identified 84 conserved and non-conserved miRNAs (belonging to 37 miRNA families) from Cd-treated and non-treated B. napus, including 19 miRNA members that were not identified before. Some of the miRNAs were validated by RNA gel blotting. Most of the identified miRNAs were found to be differentially expressed in roots/shoots or regulated by Cd exposure. The study simultaneously identified 802 targets for the 37 (24 conserved and 13 non-conserved) miRNA families, from which there are 200, 537, and 65 targets, belonging to categories I, II, and III, respectively. In category I alone, many novel targets for miRNAs were identified and shown to be involved in plant response to Cd.

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Figures

Fig. 1.
Fig. 1.
Venn diagrams for analysis of total (A and B) and unique (C and D) miRNAs between Cd-treated (S+Cd) and Cd-free (S–Cd) shoots (A and C) or between Cd-treated (R+Cd) and Cd-free (R+Cd) roots (B and D) of B. napus (this figure is available in colour at JXB online).
Fig. 2.
Fig. 2.
Validation of 14 newly identified miRNAs from roots and shoots of B. napus exposed to Cd. Two-week-old seedlings (two true leaves) were exposed to 0, 40, or 80 µM Cd for 6, 24, or 48 h, as described in Materials and methods. Total RNA from each treatment was extracted, pooled, and determined by RNA gel blotting. R–Cd, Cd-free roots; R+Cd, Cd-treated roots; S–Cd, Cd-free shoots; S+Cd, Cd-treated shoots.
See this image and copyright information in PMC

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