ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2018
A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
39 citing papers in PubMed, 88 citations in OpenAlex.
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- Exploring Gene Expression and Alternative Splicing in Duck Embryonic Myoblasts via Full-Length Transcriptome Sequencing.Veterinary sciences · 2024Article
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- Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- A Comparative Full-Length Transcriptome Analysis Using Oxford Nanopore Technologies (ONT) in Four Tissues of Bovine Origin.Animals : an open access journal from MDPI · 2024Article
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- Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Animals : an open access journal from MDPI · 2023Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- SMRT Sequencing Technology Was Used to Construct theInsects · 2023Article
- Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits.BMC biology · 2022Article
- In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing.Viruses · 2022Article
- Genome-wide annotation of protein-coding genes in pig.BMC biology · 2022Article
- Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents.Biomolecules · 2022Article
- SMRT Sequencing Reveals Candidate Genes and Pathways With Medicinal Value inFrontiers in genetics · 2022Article
- Full-length transcriptome sequencing and comparative transcriptome analysis ofFrontiers in cellular and infection microbiology · 2022Article
- High quality genome assembly of the amitochondriate eukaryoteMicrobial genomics · 2021Article
- Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits.Current issues in molecular biology · 2021Article
- Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm.BMC genomics · 2021Article
- Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs.Porcine health management · 2021Article
- Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.Genome research · 2021Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.