Abstract
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.
Highlights
Domestic pig (Sus scrofa) is an agriculturally important species and an attractive biomedical model because of its anatomical, physiological, pathological and genomic similarities to humans.[1,2] increasing number of studies have shown that reference genomes are often incomplete and has annotation and structural defects.[3,4]reference assembly and gene annotations require refinement
We found that only 1.10% (2,254/206,756) FL non-chimetric (FLNC) were
Following the latest methodologies in analysing PacBio transcriptome data, we obtained 389,781 high-quality FLNC reads, with 77,075 isoforms covering 39,940 loci, 97,727 Alternative splicing (AS) events corresponding to 2,637 models, 711 fusion isoforms and 4,394 novel lincRNAs that were not previously annotated in pig
Summary
Domestic pig (Sus scrofa) is an agriculturally important species and an attractive biomedical model because of its anatomical, physiological, pathological and genomic similarities to humans.[1,2] increasing number of studies have shown that reference genomes are often incomplete and has annotation and structural defects.[3,4]. Reference assembly and gene annotations require refinement. Obtained through short-read sequencing, the sequence data of several species have been accumulated in recent years. The knowledge on full-length (FL) sequences of mRNAs remains scarce. In some cases, low-quality transcripts derived from short-read sequencing can result in incorrect annotations.[5]
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