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A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing
Li, Yao1; Fang, Chengchi1; Fu, Yuhua1; Hu, An1; Li, Cencen1; Zou, Cheng1; Li, Xinyun1; Zhao, Shuhong1; Zhang, Chengjun2; Li, Changchun1
2018-08-01
发表期刊DNA RESEARCH
ISSN1340-2838
卷号25期号:4页码:421-437
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.
关键词single-molecule sequencing full-length novel gene alternative splicing methylation
资助信息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
DOI10.1093/dnares/dsy014
语种英语
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
WOS类目Genetics & Heredity
WOS记录号WOS:000442930900008
出版者OXFORD UNIV PRESS
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文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/62094
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
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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.
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