IrCLIP of SRSF3 in a mouse epicardial cell line
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB53737 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9871494.fastq.gz | Fastqsanger.gz | |||
| ERR9871495.fastq.gz | Fastqsanger.gz | |||
| ERR9871496.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:This experiment aims to map SRSF3 binding to the global transcriptome in a mouse epicardial cell line
2022-12-31 | E-MTAB-11853 | biostudies-arrayexpress
Project description:The epicardium is a fundamental regulator of cardiac development and regeneration, functioning to secrete essential growth factors and to produce epicardium-derived cells (EPDCs) that contribute most coronary mural cells and cardiac fibroblasts. The molecular mechanisms controlling epicardial formation have not been fully elucidated. In this study, we found that the RNA-binding protein SRSF3 is highly expressed in the embryonic proepicardium and epicardial layer. Deletion of Srsf3 from the murine proepicardium led to proliferative arrest, which prevented proper epicardial formation. Induction of Srsf3 deletion after the proepicardial stage resulted in impaired epicardial proliferation and EPDC formation by E13.5. Single-cell RNA-sequencing showed SRSF3-depleted epicardial cells were eliminated, however, the surviving non-recombined cells became hyperproliferative and, remarkably, compensated for the early deficit, via a mechanism that involved Srsf3 up-regulation This unexpected finding attests the importance of SRSF3 in controlling epicardial proliferation, and highlights the significant confounding effect of mosaic recombination on embryonic phenotyping. Mapping the SRSF3–RNA interaction network by endogenous irCLIP identified binding to major cell cycle regulators, such as Ccnd1 and Map4k4, with both splicing and non-splicing roles. This research defines SRSF3 as a key regulator of epicardial cell proliferation.
2026-02-19 | GSE313583 | GEO
Project description:We performed irCLIP-seq to determine the mRNA targets of YTHDF2 in mouse hematopoietic progenitor cell line HPC-7
2018-08-17 | GSE107953 | GEO
Project description:Background: The epicardium is a fundamental regulator of cardiac development, functioning to secrete essential growth factors and to produce epicardium-derived cells (EPDCs) that contribute most coronary vascular smooth muscle cells and cardiac fibroblasts. The molecular mechanisms that control epicardial formation and proliferation have not been fully elucidated. In this study, we found that the RNA-binding protein SRSF3 is highly expressed in the proepicardium and later in the epicardial layer during heart development. Methods: We performed scRNA-seq analyses on epicardial and epicardial-derived cells from E13.5 Wt1CreERT2;Srsf3+/+ (control), E13.5 Wt1CreERT2;Srsf3fl/fl (mutant) and E15.5 Wt1CreERT2;Srsf3fl/fl (mutant) embryonic hearts in order to elucidate the role of SRSF3 in the epicardial lineage. Results: Induction of SRSF3 deletion using Wt1CreERT2 resulted in impaired epicardial proliferation and EPDC formation at E13.5. Single-cell RNA-sequencing showed SRSF3-depleted epicardial cells were eliminated by E15.5 and the remaining non-recombined cells up-regulated Srsf3 to become hyperproliferative and compensate for the early deficit. This research identifies SRSF3 as a master regulator of epicardial cell proliferation. E15.5 control raw data already available under GSE145832
2026-02-10 | GSE205797 | GEO
Project description:Identify m6A modified residues by m6A-irCLIP in polyA selected RNA from mouse CD4+ T cells
2018-02-14 | GSE107055 | GEO
Project description:Single cell RNA sequencing (scRNA-Seq) is applied to charaterize the pro-epicardial cells (proEpiCs) in mouse pro-epicardial organ (PEO).
2020-04-04 | GSE148040 | GEO
Project description:m6A-irCLIP of mouse CD4+ T cell RNA
| PRJNA418923 | ENA
Project description:RNA binding proteins (RBPs) interact with RNA targets to control an array of processes, including RNA splicing, stability, transport, and translation1-3. Dysfunctional RNA-RBP interactions contribute to pathogenesis of a plethora of human diseases1,4,5, underscoring the need for a greater understanding of the nature and dynamics of RNA-protein assemblies. The capacity to study native RNA-dependent protein assemblies in living cells, however, has been limited. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with specific RBPs of interest. irCLIP-RNP defined landscapes of complex and multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP associations on RNA. This included cell-type-selective patterned relationships between RDAPs and primary RBPs, such as cell context-dependent reciprocal impacts of HNRNPU and NONO on each other’s RDAP landscapes. irCLIP-RNP also defined dynamic RDAP remodeling patterns in response to epidermal growth factor (EGF) and uncovered EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of mRNAs that mediate cell proliferation. The development of sequential immunoprecipitation irCLIP (RE-irCLIP) supported the same-RNA-molecule co-localization of irCLIP-RNP-identified associations. Thus, irCLIP-RNP and RE-irCLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.
2025-01-28 | PXD053494 | Pride