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

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Yao LiChangchun Li

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 tha...Continue Reading

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Citations

Jul 30, 2019·Database : the Journal of Biological Databases and Curation·Jochen T BickStefan Bauersachs
Jul 6, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Xiu FengYifeng Chen
Aug 14, 2019·Scientific Reports·Federica MattucciRomolo Caniglia
Sep 11, 2020·Bioinformatics·Lucile BroseusWilliam Ritchie
Oct 15, 2019·Frontiers in Genetics·Dóra TombáczZsolt Boldogkői
Apr 8, 2020·BioMed Research International·Lulu DengChangchun Li
Nov 26, 2020·Scientific Reports·Norbert MoldovánZsolt Boldogkői
Dec 25, 2021·Microbial Genomics·Sebastian Cristian TreitliVladimír Hampl

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