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ABSTRACT: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms

PROVIDER: PRJNA791394 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17299415_1.fastq.gz	Fastqsanger.gz
	SRR17299416_1.fastq.gz	Fastqsanger.gz
	SRR17299417_1.fastq.gz	Fastqsanger.gz
	SRR17299418_1.fastq.gz	Fastqsanger.gz
	SRR17299419_1.fastq.gz	Fastqsanger.gz

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The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Project description:Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop a computational tool, SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.

2016-11-10 | GSE79802 | GEO

Schizosaccharomyces pombe

Project description:The dynamic landscape of fission yeast meiosis alternative-splice isoforms

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A proteogenomic atlas of the human neural retina

Project description:The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing factors. However, this technique provides limited information about transcript isoforms. To gain a deeper understanding of the human neural retina and its isoforms, we generated a proteogenomic atlas that combined PacBio long-read RNA-sequencing data with mass-spectrometry and whole-genome sequencing data from three healthy human neural retina samples. RNA-sequencing revealed that one-third of all transcripts were novel, and for IRD-associated genes, even 43% were novel. The most common novel elements of these transcripts were alternative poly(A) sites, exon elongation, and intron retention. Some novel elements affect the non-coding region but for more than 50% of the novel transcripts a novel open reading frame was predicted. Using proteomics, ten novel peptides confirmed novel isoforms in five genes. Additionally, we found novel isoforms of IMPDH1, an IRD-associated gene, with supporting peptide evidence. This study provides a comprehensive overview of the transcript and protein isoforms expressed in the healthy human neural retina. Moreover, it highlights the importance of studying tissue specific transcriptomes in greater detail to better understand tissue-specific regulation and to identify disease-causing variants.

2024-10-17 | PXD045187 | Pride

Dsk1 phosphorylates Rad52 in vivo and in vitro

Project description:Serine-Arginine Protein Kinases (SRPKs) play important role in diverse biological processes such as alternative splicing and cell cycle. However, the functions and mechanisms of SRPKs in DNA damage response and repair remain unclear. Here we characterized the DNA repair function of SRPKs homolog Dsk1 in the fission yeast Schizosaccharomyces pombe.

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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Project description:This SuperSeries is composed of the following subset Series: GSE34992: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splice array) GSE34993: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) GSE34995: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq) Refer to individual Series

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Project description:The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein–RNA complex – the spliceosome – plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner.

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