Natural antisense transcripts are significantly involved in regulation of drought stress in maize.
Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS.
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.|Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA.
Jie
J
Xu
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Qi
Q
Wang
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA.
Micheal
M
Freeling
International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico.
Xuecai
X
Zhang
International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico.|Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian, Beijing 100081, China.
Yunbi
Y
Xu
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Yan
Y
Mao
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Xin
X
Tang
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Fengkai
F
Wu
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Hai
H
Lan
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Moju
M
Cao
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Tingzhao
T
Rong
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
Damon
D
Lisch
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.|Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
Yanli
Y
Lu
D000064:Acclimatization / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000378:metabolism; D055864:Droughts; D006657:Histones / Q000378:metabolism; D016372:RNA, Antisense / Q000096:biosynthesis; D018749:RNA, Plant / Q000096:biosynthesis; D013312:Stress, Physiological; D003313:Zea mays / Q000235:genetics*
D002843:Chromatin; D004251:DNA Transposable Elements; D018744:DNA, Plant; D006657:Histones; D016372:RNA, Antisense; D018749:RNA, Plant