Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

• Published in: BMC plant biology 2013-12, Vol.13 (1), p.208-208, Article 208
• Main Authors: Yu, Xiang, Yang, Jun, Li, Xiaorong, Liu, Xuxin, Sun, Chuanbao, Wu, Feijie, He, Yuke
• Format: Article
• Language: English
• Subjects: Antisense RNA; Arabidopsis thaliana; Biosynthesis; Brassica; Brassica - genetics; Brassica rapa; Deoxyribonucleic acid; DNA; DNA methylation; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic transcription; Genomes; Genomics; Heat; Hot Temperature; Methods; MicroRNAs; Real-Time Polymerase Chain Reaction; RNA polymerase; RNA sequencing; RNA, Antisense - genetics; RNA, Small Interfering - genetics; Sperm; Stress (Physiology)
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/1471-2229-13-208

Brassica rapa includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and cis-NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in B. rapa are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in B. rapa. Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in B. rapa. Analyses of four RNA sequencing datasets revealed 1031 cis-NATs B. rapa ssp. chinensis cv Wut and B. rapa ssp. pekinensis cv. Bre. Based on sequence homology between Arabidopsis thaliana and B. rapa, 303 conserved cis-NATs in B. rapa were found to correspond to 280 cis-NATs in Arabidopsis; the remaining 728 novel cis-NATs were identified as Brassica-specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150 cis-NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated. Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in B. rapa; these sRNAs are potentially useful for the genetic improvement of heat tolerance in B. rapa and other crops.