Dataset Information

Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene.

ABSTRACT: Faustoviruses are the first giant viruses of amoebae isolated on Vermamoeba vermiformis. They are distantly related to African swine fever virus, the causative agent of lethal hemorrhagic fever in domestic pigs. Structural studies have shown the presence of a double protein layer encapsidating the double-stranded DNA genome of Faustovirus E12, the prototype strain. The major capsid protein (MCP) forming the external layer has been shown to be 645-amino acid-long. Unexpectedly, its encoding sequence has been found to be scattered along a 17 kbp-large genomic region. Using RNA-seq, we studied expression of Faustovirus E12 genes at nine time points over its entire replicative cycle. Paired-end 250 bp-long read sequencing on MiSeq instrument and double-round spliced alignment enabled the identification of 26 different splice-junctions. Reads corresponding to junctions represented 2% of mapped reads and mostly matched with the predicted MCP encoding sequences. Moreover, our study enabled describing a 1,939 bp-long transcript that corresponds to the MCP, delineating 13 exons. At least two types of introns coexist in the MCP gene: group I introns that can self-splice (n = 5) and spliceosome-like introns with non-canonical splice sites (n = 7). All splice-sites were non-canonical with five types of donor/acceptor splice-sites among which AA/TG was the most frequent association.

SUBMITTER: Cherif Louazani A

PROVIDER: S-EPMC6247863 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene.

Cherif Louazani Amina A Baptiste Emeline E Levasseur Anthony A Colson Philippe P La Scola Bernard B

Frontiers in microbiology 20181023

Faustoviruses are the first giant viruses of amoebae isolated on <i>Vermamoeba vermiformis</i>. They are distantly related to African swine fever virus, the causative agent of lethal hemorrhagic fever in domestic pigs. Structural studies have shown the presence of a double protein layer encapsidating the double-stranded DNA genome of Faustovirus E12, the prototype strain. The major capsid protein (MCP) forming the external layer has been shown to be 645-amino acid-long. Unexpectedly, its encodin ...[more]

PMID: 30487777

Similar Datasets

Project description:Alternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as nr5a1 and ddx4, have sex-biased transcripts between males and females, suggesting a potential regulatory role of alternative splicing in gonads. Currently, the sex-specific alternative splicing events and genes have not been comprehensively studied at the genome-wide level in zebrafish. In this study, through global splicing analysis on three independent sets of RNA-seq data from matched zebrafish testes and ovaries, we identified 120 differentially spliced genes shared by the three datasets, most of which haven't been reported before. Functional enrichment analysis showed that the GO terms of mRNA processing, mRNA metabolism and microtubule-based process were strongly enriched. The testis- and ovary-biased alternative splicing genes were identified, and part of them (tp53bp1, tpx2, mapre1a, kif2c, and ncoa5) were further validated by RT-PCR. Sequence characteristics analysis suggested that the lengths, GC contents, and splice site strengths of the alternative exons or introns may have different influences in different types of alternative splicing events. Interestingly, we identified an unexpected high proportion (over 70%) of non-frameshift exon-skipping events, suggesting that in these cases the two protein isoforms derived from alternative splicing may both have functions. Furthermore, as a representative example, we found that the alternative splicing of ncoa5 causes the loss of a conserved RRM domain in the short transcript predominantly produced in testes. Our study discovers novel sex-specific alternative splicing events and genes with high reliabilities in zebrafish testes and ovaries, which would provide attractive targets for follow-up studies to reveal the biological significances of alternative splicing events and genes in sex determination and gonadal differentiation.

Dataset Information

Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene.

Publications

Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets