RNA-seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling
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ABSTRACT:
PROVIDER: PRJEB58983 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10782549_1.fastq.gz | Fastqsanger.gz | |||
| ERR10782549_2.fastq.gz | Fastqsanger.gz | |||
| ERR10782550_1.fastq.gz | Fastqsanger.gz | |||
| ERR10782550_2.fastq.gz | Fastqsanger.gz | |||
| ERR10782551_1.fastq.gz | Fastqsanger.gz |
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Project description:Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia-Absent Radius (TAR) Syndrome is a rare congenital disease presenting with reduced blood platelets (megakaryocytic thrombocytopenia) and forelimb anomalies, concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing, transport, and nonsense-mediated decay. How perturbing a general mRNA-processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here, we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity (PCP) signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function, we find a significant reduction of cd41-positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a-mutant zebrafish embryos already after gastrulation accumulate mRNAs with erroneously included introns, a hallmark of defective nonsense-mediated decay. Affected mRNAs include transcripts encoding components of the non-canonical Wnt pathway involved in PCP signaling, and rbm8a mutant-embryos show hallmarks of Wnt/PCP-dependent, early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b, wnt11f2, fzd7a, and vangl2. Following axis formation, rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm (LPM) that forms the hematopoietic, cardiovascular, kidney, and forelimb skeleton progenitors. Subsequently, rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a, kdrl, sox7, and the megakaryocyte regulator gfi1aa. Lastly, we document similar hematopoietic defects upon loss of vangl2. Together, our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.
2023-03-31 | E-MTAB-12503 | biostudies-arrayexpress
Project description:Defects in blood development frequently occur among syndromic congenital anomalies. Thrombocytopenia-Absent Radius (TAR) syndrome is a rare congenital condition with reduced platelets (hypomegakaryocytic thrombocytopenia) and forelimb anomalies, concurrent with more variable heart and kidney defects. TAR syndrome associates with hypomorphic gene function for RBM8A/Y14 that encodes a component of the exon junction complex involved in mRNA splicing, transport, and nonsense-mediated decay. How perturbing a general mRNA-processing factor causes the selective TAR Syndrome phenotypes remains unknown. Here, we connect zebrafish rbm8a perturbation to early hematopoietic defects via attenuated non-canonical Wnt/Planar Cell Polarity (PCP) signaling that controls developmental cell re-arrangements. In hypomorphic rbm8a zebrafish, we observe a significant reduction of cd41-positive thrombocytes. rbm8a-mutant zebrafish embryos accumulate mRNAs with individual retained introns, a hallmark of defective nonsense-mediated decay; affected mRNAs include transcripts for non-canonical Wnt/PCP pathway components. We establish that rbm8a-mutant embryos show convergent extension defects and that reduced rbm8a function interacts with perturbations in non-canonical Wnt/PCP pathway genes wnt5b, wnt11f2, fzd7a, and vangl2. Using live-imaging, we found reduced rbm8a function impairs the architecture of the lateral plate mesoderm (LPM) that forms hematopoietic, cardiovascular, kidney, and forelimb skeleton progenitors as affected in TAR Syndrome. Both mutants for rbm8a and for the PCP gene vangl2 feature impaired expression of early hematopoietic/endothelial genes including runx1 and the megakaryocyte regulator gfi1aa. Together, our data propose aberrant LPM patterning and hematopoietic defects as consequence of attenuated non-canonical Wnt/PCP signaling upon reduced rbm8a function. These results also link TAR Syndrome to a potential LPM origin and a developmental mechanism.
| S-EPMC10120739 | biostudies-literature
Project description:In this study, we aimed to investigate the impact of RBM8A knockdown on mRNA expression in gastric cnacer cells. We used RNAi technology to specifically knock down RBM8A expression in AGS cells, establishing two experimental groups: siNC and siRBM8A. Each group had three biological replicates. Subsequently, mRNA-seq was performed to comprehensively analyze the mRNA expression profiles of the cells after RBM8A knockdown. Our results may provide insights into the biological functions of RBM8A in gastric cancer and potential therapeutic targets.
2025-04-17 | GSE292234 | GEO
Project description:RBM8A is an RNA-binding protein. To identify RNAs interacting with RBM8A, we employed RNA immunoprecipitation (RIP) to enrich associated RNAs, followed by high-throughput sequencing and bioinformatics approaches to characterize the RBM8A-bound RNA profile.
2025-04-17 | GSE292233 | GEO
Project description:The impact of acute RBM8A depletion on nascent transcription (using the auxin (IAA)-inducible degron system in conjunction with 4sU-sequencing) was investigated.
2022-07-13 | GSE207898 | GEO
Project description:Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole cell acetate uptake rates (WAUR) and cell viability, and for gene expression changes using Affymetrix GeneChip technology and RT-PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multi-drug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant. Keywords: stress response to pentachlorophenol
2006-09-08 | GSE5604 | GEO
Project description:PCP remediation bioreactors Raw sequence reads
| PRJNA475524 | ENA
Project description:Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole cell acetate uptake rates (WAUR) and cell viability, and for gene expression changes using Affymetrix GeneChip technology and RT-PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multi-drug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant. Experiment Overall Design: Cells of P. aeruginosa were grown in steady-state nutrient-limiting conditions using a minimal medium with acetate as the sole carbon source. PCP was added as a continuous input, and the samples were taken at timepoints corresponding to approximately 0.5, 1, and 2 generation times. Reactors were run at least in triplicate, and samples from duplicate WT reactors and a single RpoS- reactor were used for the microarrays. Gene expression is reported as the average fold-change associated with gene expression of PCP-shocked cells compared with the pre-PCP timepoint (0 hours) for the WT.
2008-06-13 | E-GEOD-5604 | biostudies-arrayexpress
Project description:The series represents the analysis data of four TAR syndrome patients by submegabase resolution BAC array. Keywords: array CGH
2007-01-07 | GSE5781 | GEO