A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon

doi:10.1186/gb-2013-14-8-r92

	A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
	Zhang, Jingyu; Mao, Zhiwei; Chong, Kang
	2013
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	14 期号:8
摘要	Background: mRNA degradation is a critical factor in determining mRNA abundance and enables rapid adjustment of gene expression in response to environmental stress. The involvement of processing bodies in stress response suggests a role for decapping-mediated mRNA degradation. However, little is known about the role of mRNA degradation under stressful environmental conditions. Results: Here, we perform a global study of uncapped mRNAs, via parallel analysis of RNA ends (PARE), under cold stress in Brachypodium distachyon. Enrichment analysis indicates that degradation products detected by PARE are mainly generated by the decapping pathway. Endonucleolytic cleavages are detected, uncovering another way of modulating gene expression. PARE and RNA-Seq analyses identify four types of mRNA decay patterns. Type II genes, for which light-harvesting processes are over-represented in gene ontology analyses, show unchanged transcript abundance and altered uncapped transcript abundance. Uncapping-mediated transcript stability of light harvesting-related genes changes significantly in response to cold stress, which may allow rapid adjustments in photosynthetic activity in response to cold stress. Transcript abundance and uncapped transcript abundance for type III genes changes in opposite directions in response to cold stress, indicating that uncapping-mediated mRNA degradation plays a role in regulating gene expression. Conclusion: To our knowledge, this is the first global analysis of mRNA degradation under environmental stress conditions in Brachypodium distachyon. We uncover specific degradation and endonucleolytic cleavage patterns under cold stress, which will deepen our understanding of mRNA degradation under stressful environmental conditions, as well as the cold stress response mechanism in monocots.
关键词	mRNA stability decapping cold stress PARE Brachypodium distachyon
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/gb-2013-14-8-r92
收录类别	SCI
语种	英语
WOS关键词	LOW-TEMPERATURE ; P-BODIES ; GENE-EXPRESSION ; PARALLEL ANALYSIS ; PROTEIN-KINASE ; WIDE ANALYSIS ; IDENTIFICATION ; ARABIDOPSIS ; PHOTOSYNTHESIS ; MICRORNAS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000328195400010
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of China(National Natural Science Foundation of China (NSFC)) ; Main Direction Program of Knowledge Innovation of Chinese Academy of Sciences(Chinese Academy of Sciences)
作者邮箱	Zhang, Jingyu/AAL-4934-2021
作品OA属性	Green Published, hybrid
引用统计	被引频次：19[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27794
专题	中科院植物分子生理学重点实验室
作者单位	Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jingyu,Mao, Zhiwei,Chong, Kang. A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon[J]. GENOME BIOLOGY,2013,14(8).
APA	Zhang, Jingyu,Mao, Zhiwei,&Chong, Kang.(2013).A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon.GENOME BIOLOGY,14(8).
MLA	Zhang, Jingyu,et al."A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon".GENOME BIOLOGY 14.8(2013).

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