Ontology highlight
ABSTRACT:
PROVIDER: PRJNA930469 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23308049_1.fastq.gz | Fastqsanger.gz | |||
| SRR23308049_2.fastq.gz | Fastqsanger.gz | |||
| SRR23308050_1.fastq.gz | Fastqsanger.gz | |||
| SRR23308050_2.fastq.gz | Fastqsanger.gz |
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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.
2024-10-31 | MODEL2410300001 | BioModels
Project description:We identified PRP4 kinase-A (PRP4ka) in a forward genetic screen based on an alternatively-spliced GFP reporter gene in Arabidopsis thaliana (Arabidopsis). Prp4 kinase, which was the first spliceosome-associated kinase shown to regulate splicing in fungi and mammals, has not yet been studied in plants. Analysis of RNA-seq data from the prp4ka mutant revealed widespread perturbations in alternative splicing. A quantitative iTRAQ-based phosphoproteomics investigation of the mutant identified phosphorylation changes in several serine/arginine-rich proteins, which regulate constitutive and alternative splicing, as well as other splicing-related factors. The results demonstrate the importance of PRP4ka in alternative splicing and suggest that PRP4ka may influence alternative splicing patterns by phosphorylating a subset of splicing regulators.
2018-10-25 | PXD008580 | Pride
Project description:PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQBP1 as an important alternative splicing effector necessary for maintaining normal neuron functions in the brain. In order to explore PQBP1's functions in alternative splicing regulation and neuronal activities, we systematically profiled the alternative splicing targets of PQBP1 in mouse embryonic cortical neurons by RNA-seq. The mRNAs whose alternative splicing are affected by PQBP1 showed tissue-specific functional enrichment especially in neurite outgrowth, with strong Gene Ontology (GO) enrichments for neuron projection development/morphogenesis, dendrite development and axonogenesis. PQBP1's alternative splicing targets are also functionally enriched in RNA splicing, chromatin modification, and ARF signal transduction. We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.
2013-03-15 | E-GEOD-44402 | biostudies-arrayexpress
Project description:Alternative splicing is critical for development. However, its role in the specification of the three embryonic germ layers is poorly understood. By performing RNA-Seq on human embryonic stem cells (hESCs) and derived endoderm, cardiac mesoderm, and ectoderm cell lineages, we detect distinct alternative splicing programs associated with each lineage. The most prominent splicing program differences are observed between definitive endoderm and cardiac mesoderm. Integrative multi-omics analyses link each program with lineage-specific RNA binding protein regulators, and further suggest a widespread role for Quaking (QKI) in the specification of cardiac mesoderm. Remarkably, knockout of QKI disrupts the cardiac mesoderm-associated alternative splicing program and formation of myocytes. These changes likely arise in part through reduced expression of BIN1 splice variants linked to cardiac development. Collectively, our results thus uncover alternative splicing programs associated with the three germ lineages and demonstrate an important role for QKI in the formation of cardiac mesoderm.
2022-02-01 | MSV000088762 | MassIVE
Project description:<p>RNA sequencing was performed on human DRGs and relative gene abundances were calculated.</p> <p>Various analyses were performed:</p> <p> <ol> <li>Human DRG gene expression profiles were contrasted with a panel of gene expression profiles of relevant tissues in human and mouse ( integrating, among other sources, datasets from ENCODE and GTex ) in order to identify.</li> <ol type="a"> <li>DRG-enriched gene expression, co-expression modules of DRG-expressed genes, and key transcriptional regulators in humans.</li> <li>Contrasting the human and mouse DRG transcriptomes to identify DRG-enriched gene expression patterns that were conserved between human and mouse, identifying putative cell types of expression of these genes, and potential known drugs that might target the corresponding gene products.</li> <li>Characterization of non-coding RNA profile of human and mouse DRGs.</li> <li>Characterization of DRG-enriched alternative splicing and alternative transcription start site usage based transcript variants in humans and mouse, and the overlap between these two species.</li> <li>Contrasting of human DRG and GTex human tibial nerve samples to identify putative axonally transported mRNAs in sensory neurons.</li> </ol> <li>Human DRG transcriptomes from donors suffering from neuropathic and/or chronic pain were contrasted with controls to identify.</li> <ol type="a"> <li>Differentially expressed genes, pathways and regulators path play a potential role in neuronal plasticity, electrophysiological activity, immune signaling and response.</li> <li>Predictive models (Random Forests) were built to jointly predict the sex and pain state of samples based on information contained solely in autosomal gene expression profile.</li> <li>Gene co-expression modules were identified and gene set enrichment analysis performed.to identify sample - pathway associations, and to broadly characterize plasticity in human DRG cell types.</li> </ol> </ol> </p>
| phs001158 | dbGaP
Project description:Mammalian development is an intricate process regulated by multiple gene isoforms and their epigenetic states, which are yet undefined. Using integrative massive parallel sequencing and bioinformatics approach, we built genome-wide inventory of transcript variants, their promoters and histone modification states during normal development, using mouse cerebellum as model system. The data we integrated consists of 29,589 (4,792 novel) promoters that transcribe 61,525 (12,796 novel) distinct mRNAs, corresponding to 14,508 protein-coding and 9,862 non-coding genes. While 68% of the multi-transcript genes exhibit alternative splicing, 78% use alternative transcriptional events that are regulated during cerebellar development through H3K4me3 and H3K27me3. The data presented highlight the magnitude of alternative promoters and transcriptional termination as major source of transcriptome diversity along with alternative splicing. We also show that alternative promoters differentially activated during normal cerebellar development are aberrantly used in medulloblastoma, emphasizing the importance of studying gene regulation and function at the isoform-level. Study of transcriptome diversity in cerebellar development. We performed mRNA-seq and ChIP-seq experiments. mRNA-seq were performed on total RNA isolated from two P0, P5, P15 and adult cerebellum using 10 microgram of total RNA as the starting material for sequencing library prep. For each stage, mRNA-seq data was obtained from two lanes of a flowcell. For ChIP-seq experiments, solubilized chromatin was prepared by pooling multiple cerebellum tissues (3-18) and then ChIP-enriched DNA (using anti-RNAP II, anti-H3K4me3, anti-H3K27me3, or negative control IgG antibodies) were isolated. 10 microgram of ChIP-enriched DNA was used to prepare the ChIP-seq library for sequencing in a single lane.
2011-06-07 | E-GEOD-23525 | biostudies-arrayexpress
Project description:Mitosis deregulation is a key event during carcinogenesis. Alternative splicing spectrum alteration plays a critical role during mitosis shift. However, the molecules responsible for dysregulated alternative splicing driving carcinogenetic mitosis remain poorly defined. Here, we demonstrate that cancer metastasis-associated antigen 1 (MTA1), a well-known oncogenic chromatin modifier, broadly interacts and co-expresses with RBPs across cancers, contributes to cancerous mitosis-related alternative splicing. Using developed fCLIP-seq technology, we show that MTA1 binds abundant transcripts, preferentially at splicing-responsible motifs, influencing both the abundance and alternative splicing (AS) of target transcripts. MTA1 is cytoplasmic and extrachromosomal at mitosis. Through the RNA-association activity, MTA1 regulates the mRNA level and guides the AS of a serious of mitosis regulators to control the mitosis. MTA1 deletion abrogated the dynamic AS switches of variants for ATRX and MYBL2 at mitotic stage, which are relevant to mitosis and tumorigenesis. MTA1 dysfunction causes a defective mitotic arrest, leading to aberrant chromosome segregation, and resultantly chromosomal instability (CIN) in cancer cells and tissues, which eventually contributes to tumorigenesis. Currently, little is known about the RNA splicing during mitosis, here, we present MTA1 as a pivotal RNA-binding protein, functioning to orchestrate the dynamic splicing of mitosis regulators linked to mitosis control in tumorigenesis.
2020-03-30 | PXD018242 |
Project description:Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. Further, alternative splicing of human NAGNAGs was associated with an order of magnitude increase in the frequency of exon length changes at orthologous mouse/rat exon boundaries, suggesting that NAGNAGs accelerate exon evolution. Together, our analyses show that NAGNAG alternative splicing constitutes a major generator of tissue-specific proteome diversity and accelerates evolution of proteins at exon-exon boundaries. mRNA-Seq of sixteen human and eight mouse tissues. Supplementary files: human.nagnag.junctions.gff and mouse.nagnag.junctions.gff are the annotation files (in GFF3 format) corresponding to the 'bwtout' mapped reads files linked to the Sample records. Raw data files provided for Samples GSM742937-GSM742952 only.
2012-01-05 | E-GEOD-30017 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE25287: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (expression) GSE25494: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (ChIP-Seq) Refer to individual Series
2010-12-09 | E-GEOD-25495 | biostudies-arrayexpress
Project description:Huntingtonâs disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component however has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of 7 human HD brains and 7 controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using an expanded panel of 54 brain tissues from patients and controls, we also identified 9 splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD RNA-seq analysis of the BA4 motor cortex of 7 control and 7 Huntington's disease patients. 1.5 ug of total RNA was used for RNA-seq library preparation using the TruSeq⢠Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.
2016-06-14 | E-GEOD-79666 | biostudies-arrayexpress