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Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development (bulk)

ABSTRACT: Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development (bulk)

PROVIDER: PRJNA615168 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11420400_1.fastq.gz	Fastqsanger.gz
	SRR11420400_2.fastq.gz	Fastqsanger.gz
	SRR11420401_1.fastq.gz	Fastqsanger.gz
	SRR11420401_2.fastq.gz	Fastqsanger.gz
	SRR11420402_1.fastq.gz	Fastqsanger.gz

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Characterization of splice isoform switching during human kidney development

Project description:Characterization of splice isoform switching during human kidney development

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Characterization of splice isoform switching during human kidney development

Project description:Background: Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme – a transient kidney-specific progenitor state – undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms’ tumor that mimics normal kidney development. While human kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. Methods: We performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms’ tumor patient-derived xenografts. Results: We identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms’ tumors. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate mRNA splice isoform switching during human kidney development. Conclusions: These findings illuminate new molecular mechanisms involved in human kidney development and pediatric kidney tumors.

2022-11-14 | GSE150684 | GEO

Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

Project description:Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

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Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development (bulk)

Project description:Kidney development is a complex process involving multiple interacting and transforming cell types. These cell types were recently characterized using the Drop-seq single-cell technology for measuring gene expression from many thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of cellular heterogeneity that cannot be measured with the Drop-seq technology. This study describes the use of full transcript length single-cell RNA sequencing to characterize alternative splicing in the developing mouse fetal kidney; in particular, the identification of genes that are alternatively spliced during the transition from mesenchymal to epithelial cell states, as well as their splicing regulators. These results improve our understanding of the molecular mechanisms involved in kidney development.

2020-07-27 | GSE147525 | GEO

Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

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Isoform switching events in esophageal adenocarcinoma progression

Project description:Isoform switching events in esophageal adenocarcinoma progression

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Isoform switching events in esophageal adenocarcinoma progression

Project description:Global isoform switching in esophageal adenocarcinoma (EAC) or precursor lesions has not been previously characterized. This form of alternative splicing has recently been recognized as highly prevalent in multiple other cancers. In this study, isoform switch analysis was performed using next generation sequencing of RNA isolated from patient tissues across a histopathological continuum, ranging from low risk Barrett’s esophagus (BE) to BE with advanced dysplasia. Patients were stratified based on esophageal tissue histopathology.

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A conserved germline-specific Dsn1 alternative splice isoform supports oocyte and embryo development

Project description:Alternative RNA splicing can generate distinct protein isoforms to allow for the differential control of cell processes across cell types. The chromosome segregation and cell division programs associated with somatic mitosis and germline meiosis display dramatic differences such as kinetochore orientation, cohesin removal, or the presence of a gap phase. These changes in chromosome segregation require alterations to the established cell division machinery. However, it remains unclear what aspects of kinetochore function and its regulatory control differ between the mitotic and meiotic cell divisions to rewire these core processes. Additionally, the alternative splice isoforms that differentially modulate distinct cell division programs have remained elusive. Here, we demonstrate that mammalian germ cells express an alternative mRNA splice isoform for the kinetochore component, DSN1, a subunit of the MIS12 complex that links the centromeres to spindle microtubules during chromosome segregation. This germline DSN1 isoform bypasses the requirement for Aurora kinase phosphorylation for its centromere localization due to the absence of a key regulatory region allowing DSN1 to display persistent centromere localization. Expression of the germline DSN1 isoform in somatic cells results in constitutive kinetochore localization, chromosome segregation errors, and growth defects, providing an explanation for its tight cell type-specific expression. Reciprocally, precisely eliminating expression of the germline-specific DSN1 splice isoform in mouse models disrupts oocyte maturation and early embryonic divisions coupled with a reduction in fertility. Together, this work identifies a germline-specific splice isoform for a chromosome segregation component and implicates its role in mammalian fertility.

2024-08-28 | PXD054119 | Pride

Identification of alternative splice variants using unique isoform-specific tryptic peptide sequences for database searches

Project description:Alternative splicing is a mechanism in eukaryotes by which different forms of messenger RNAs (mRNAs) are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database which contains only proteotypic tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to the peptide sequences that matches the unique amino acid sequence of splice variants to MS data. Furthermore, we combined this database without isoform 1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa), and phosphoproteomics studies were analyzed using these two databases. Several non-isoform 1-specific peptides were found in both cell lines, some of them seemed to be cell line specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several non-isoform 1-specific peptides and some of them showed clear quantitative differences between the two states.

2017-05-19 | PXD006026 | Pride

Development and validation of AI/ML derived splice-switching oligonucleotides

Project description:Development and validation of AI/ML derived splice-switching oligonucleotides

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