Porcine CD200R1-like splicing variants
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ABSTRACT:
PROVIDER: PRJEB48207 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Characterization od swine CD200R1 splicing variants expressed in blood monocytes
| PRJEB48195 | ENA
Project description:Purpose: Identification of genes regulating growth and fatness traits in pig. Methods: Hypothalamic transcriptome analysis through RNA-seq and differential expression analysis of divergent pigs for growth and fatness traits. Results: Characterization of the transcripts expressed in the porcine hypothalamus and identification of differentially expressed genes, some of them located within previously described QTL regions. Conclusions: Characterization of porcine hypothalamic transcriptome and identification of relevant genes and transcription factors related to the traits of interest.
2013-11-01 | GSE51968 | GEO
Project description:Purpose: Identification of genes regulating growth and fatness traits in pig. Methods: Hypothalamic transcriptome analysis through RNA-seq and differential expression analysis of divergent pigs for growth and fatness traits. Results: Characterization of the transcripts expressed in the porcine hypothalamus and identification of differentially expressed genes, some of them located within previously described QTL regions. Conclusions: Characterization of porcine hypothalamic transcriptome and identification of relevant genes and transcription factors related to the traits of interest. Transcriptome sequencing of 10 hypothamic samples of two groups of divergent pigs for growth and fatness (five per group).
2013-11-01 | E-GEOD-51968 | biostudies-arrayexpress
Project description:Single-cell RNA-Seq of porcine peripheral blood monocytes
| PRJNA1036253 | ENA
Project description:Leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) are evolutionarily conserved presynaptic cell-adhesion molecules that orchestrate multifarious synaptic adhesion pathways. Extensive alternative splicing of LAR-RPTP mRNAs, similar to neurexins, may produce innumerable LAR-RPTP isoforms that act as regulatory codes for determining the identify and strength of specific synapse signaling. However, no direct evidence for the hypothesis exists, apart from the role of LAR-RPTP splice variants in specifying region-specific, cell type-specific and neural circuit-specific properties in vivo. Here, using deep RNA sequencing (RNA-seq), we targeted Ptprs, Ptprd, and Ptprf mRNAs in diverse cell types across adult mouse brain areas. In addition to identifying novel alternatively spliced exons of Ptprd, we found pronounced cell-type-specific patterns of two microexons, meA and meB, in brain Ptprd mRNAs. Quantitative targeted proteomics uncovered profiles of LAR-RPTP proteoforms containing or lacking meA that are in line with RNA-seq results. Moreover, diverse neural circuits targeting the same neuronal popluations were dictated by the expression of different Ptprd variants characterized by distinct inclusion patterns of meA and/or meB. Remarkably, fear-related learning induced upregulation of Ptprd meA+ variants in hippocampal memory-activated dentate gyrus neurons. Furthermore, conditional ablation of Ptprd meA+ variants at presynaptic loci of distinct hippocampal circuits resulted in impairment of distinct modes of synaptic transmission and different cognitive tasks. Our data provide the first evidence of cell-type- and/or circuit-specific expression patterns and physiological functions of LAR-RPTP microexons that are dynamically regulated and likely to dictate diverse synaptic properties. In particular, we propose Ptprd splicing as a key mechanism that mediates activity-dependent neural circuit specification
2023-05-08 | MSV000091879 | MassIVE
Project description:Humans co-existed and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,224 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 969 exonic splicing mutations (ESMs) that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than in Neanderthals. Adaptively introgressed variants were enriched for moderate effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a novel tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a novel Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide novel insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.
2022-10-07 | GSE201856 | GEO
Project description:It is estimated that 10-30% of disease-associated genetic variants affect splicing. Splicing variants may generate deleteriously altered gene product and are potential therapeutic targets. However, experimental diagnosis for splicing variants is time-consuming and reliable computational prediction tools have not been established, especially for the 3’ end of introns. The major challenge lies in the redundant and ill-defined branch site motif therein. Here, we carried out unbiased massively parallel splicing assays on 5,307 disease-associated variants overlapped with branch sites. We observed that 11.0% (455 out of 4,154 valid comparisons) of candidate variants showed a consistent pattern of altered splicing across four experimental replicates, among which 244 candidates (6.1%) presented more than two-fold changes in the use of noncanonical splice sites and these are named high-confidence (HC) significant candidates.
2022-05-10 | GSE179892 | GEO
Project description:Alternative splicing is a key mechanism for expanding transcriptomic and proteomic complexity, yet its role in innate immune activation remains incompletely understood. Here, we applied Oxford Nanopore native RNA-sequencing to generate an isoform-level transcriptome of primary human monocytes before and after activation with lipopolysaccharide. We identify over 24,000 expressed isoforms, including thousands of previously unannotated variants. Activation induced widespread isoform-specific expression changes, leading to extensive isoform switching events, validated using matched short-read RNA-Seq. These activation-induced shifts enhanced transcript immune-regulatory functions: activated monocytes preferentially express longer, coding-competent isoforms with complete open reading frames, fewer retained introns, and increased domain complexity. By integrating matched Ribo-seq and proteomic data, we demonstrate that these isoform modulations are associated with enhanced translation of immune effector proteins. Together, our findings position alternative splicing as a dynamic and functional regulator of monocyte activation, emphasizing the need for isoform-level resolution to fully understand immune cell function and inflammation.
2026-04-29 | PXD070784 | Pride
Project description:Using a high throughput splicing reporter assay, we tested 1,080 single nucleotide variants in POU1F1, a key transcription factor essential for pituitary development. Our saturation splicing effect map identifies 96 splice disruptive variants, including 14 synonymous variants, of which 8 were found in unrelated patients diagnosed with hypopituitarism.
2021-04-22 | GSE172504 | GEO
Project description:SF3B1 is an essential and ubiquitous splicing factor that plays a pivotal role in the early steps of pre-mRNA splicing. Recurrent somatic missense mutations in SF3B1 are frequent in cancers, but no constitutional variant has been reported so far. We describe here a cohort of 26 individuals with neurodevelopmental disorders, harbouring SF3B1 constitutional heterozygous variants that appeared mostly de novo. Patients present with a global developmental delay, associated with variable neurological and facial dysmorphic traits. A dichotomy may emerge between patients harbouring predicted loss of function (n=9) and missense variants (n=17), the latter being associated with a more severe and syndromic phenotype, including heart and gastrointestinal anomalies. We focused on de novo SF3B1 missense variants, which were largely distinct from those reported in cancer. Functional complementation assays show that de novo SF3B1 missense variants did not cause a loss of function of the protein. Targeted and genome-wide analysis of RNA splicing reveal that they affect canonical and alternative splicing more moderately than somatic variants, and subtly modify the splicing of many transcripts, some of which are involved in neurodevelopmental disorders. SF3B1 joins the short list of U2 snRNP components involved in both cancer and neurodevelopmental disorders.
2026-01-31 | GSE287369 | GEO