Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)

doi:10.1186/1471-2164-14-280

	Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)
	Hu Zheng; Jiang Qiyan; Ni Zhiyong; Zhang Hui
刊名	BMC GENOMICS
	2013
卷号	14 页码:-
ISSN号	1471-2164
DOI	10.1186/1471-2164-14-280
通讯作者	Hu Zheng
英文摘要	Background: Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed.Results: A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1-177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.Conclusions: We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; GENETICS & HEREDITY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000318525200002
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/5048]
专题	作物科学研究所_种质资源保存与研究中心
作者单位	Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Genet Resources & Improvement, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Hu Zheng,Jiang Qiyan,Ni Zhiyong,et al. Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)[J]. BMC GENOMICS,2013,14:-.
APA	Hu Zheng,Jiang Qiyan,Ni Zhiyong,&Zhang Hui.(2013).Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max).BMC GENOMICS,14,-.
MLA	Hu Zheng,et al."Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)".BMC GENOMICS 14(2013):-.