A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing

doi:10.1093/dnares/dsy014

	A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing
	Li, Yao 1; Fang, Chengchi 1; Fu, Yuhua 1; Hu, An 1; Li, Cencen 1; Zou, Cheng 1; Li, Xinyun 1; Zhao, Shuhong 1; Zhang, Chengjun2 ; Li, Changchun 1
刊名	DNA RESEARCH
	2018-08-01
卷号	25 期号:4 页码:421-437
关键词	single-molecule sequencing full-length novel gene alternative splicing methylation
ISSN号	1340-2838
DOI	10.1093/dnares/dsy014
英文摘要	Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig. Our analysis identified an unprecedented scale of high-quality full-length isoforms with over 28,127 novel isoforms from 26,881 novel genes. More than 92,000 novel AS events were detected and intron retention predominated in AS model, followed by exon skipping. Interestingly, we found that DNA methylation played an important role in generating various AS isoforms by regulating splicing sites, promoter regions and first exons. Furthermore, we identified a large of fusion transcripts and novel lncRNAs, and found that DNA methylation of the promoter and gene body could regulate lncRNA expression. Our results significantly improved existed gene models of pig and unveiled that pig AS and epigenetic modify were more complex than previously thought.
资助项目	National Natural Science Foundation of China (NSFC)[31472076] ; Science Fund for Distinguished Young Scholars of Hubei Province of China[2014CFA024] ; Research Project of Chinese Ministry of Education[113048A]
WOS研究方向	Genetics & Heredity
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000442930900008
资助机构	National Natural Science Foundation of China (NSFC) ; Science Fund for Distinguished Young Scholars of Hubei Province of China ; Research Project of Chinese Ministry of Education
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/62093]
专题	中国科学院昆明植物研究所
通讯作者	Li, Changchun
作者单位	1.Huazhong Agr Univ, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Coll Anim Sci & Technol, Wuhan 430070, Hubei, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Li, Yao,Fang, Chengchi,Fu, Yuhua,et al. A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing[J]. DNA RESEARCH,2018,25(4):421-437.
APA	Li, Yao.,Fang, Chengchi.,Fu, Yuhua.,Hu, An.,Li, Cencen.,...&Li, Changchun.(2018).A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing.DNA RESEARCH,25(4),421-437.
MLA	Li, Yao,et al."A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing".DNA RESEARCH 25.4(2018):421-437.