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Natural antisense transcripts are significantly involved in regulation of drought stress in maize

Author: Jie Xu
Author: Qi Wang
Author: Freeling, M.
Author: Zhang, X.
Author: Yunbi Xu
Author: Yan Mao
Author: Xin Tang
Author: Fengkai Wu
Author: Hai Lan
Author: Moju Cao
Author: Tingzhao Rong
Author: Damon Lisch
Author: Yanli Lu
Year: 2017
Abstract: 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.
Format: PDF
Language: English
Publisher: Oxford University Press
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Type: Article
Place of Publication: Oxford, United Kingdom
Pages: 5126-5141
Issue: 9
Volume: 45
DOI: 10.1093/nar/gkx085
Agrovoc: MAIZE
Related Datasets:
Journal: Nucleic Acids Research

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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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