Transcript isoform switching occurs in the murine synaptic transcriptome during aging
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ABSTRACT:
PROVIDER: PRJNA611559 | ENA |
REPOSITORIES: ENA
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Project description:Preliminary Summary: In this study, we set to specifically analyze effects of aging on differential splicing in the local synaptic proteome. To this end, we analyzed the RNA extracted from synaptosomes obtained from cerebral cortices of C57BL/6 mice of 3 weeks, 5 months and 19 months of age. Synaptosomes are artificial, membranous sacs that contain synaptic components and are generated by subcellular fractionation of homogenized or ground-up nerve tissue. We employ RNA-seq using paired long-reads to obtain comprehensive sequence information on synaptic transcripts and two different bioinformatic methods (DIEGO and LeafCutter) to quantify differential splicing. Finally, the change in the usage of the selected junctions was validated through RT-qPCR and RT-PCR using an independent set of samples.
2024-03-06 | GSE146636 | GEO
Project description:Pervasive, coordinated protein level changes driven by transcript isoform switching during meiosis
| PRJNA428526 | ENA
Project description:To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous, genome-wide measurements of mRNA, translation and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases—or over 8% of all measured genes—involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether an mRNA is induced or not, but rather based on the type of transcript produced.
2018-02-22 | GSE108778 | GEO
Project description:Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 and platform with 250bp paired chemistry and analysed by IsoformSwitchAnalyseR tool of bioconductor Results: Differential transcript expression (DTE) and differential transcript utilization (DTU) of C. glabrata showed that it utilized 292 significant transcripts isoforms during biofilm formation via isoform switching process. Conclusion: Investigation of the present study elucidated that the switched isoform and predicted proteins encoded in biofilm growth mode of this pathogen could be used as a potential target for the development of novel antifungal targets.
2021-06-09 | GSE162024 | GEO
Project description:Alternative RNA 3’-end processing provides an important source of transcriptome diversification, which impacts various biological processes and the etiology of diseases, including cancer. A prime example of this is the transcript isoform switch that leads to the read-through expression of the long non-coding RNA NEAT1_2, at the expense of the shorter polyadenylated transcript NEAT1_1. Expression of NEAT1_2 is required for the formation of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. Searching for proteins that modulate this isoform switching event we identified factors involved in the 3’-end processing of polyadenylated (pA+) RNA as well as several components of the Integrator complex. Perturbation experiments established that, by promoting the cleavage of NEAT1_2, Integrator forces NEAT1_2 to NEAT1_1 isoform switching and, thereby, restrains PS assembly. Consistently, low expression levels of several Integrator subunits correlated with poorer prognosis of cancer patients exposed to chemotherapeutics. Our study identifies Integrator as a key regulator of PS biogenesis and establish a link between Integrator, cancer biology and chemosensitivity, which may be exploited therapeutically.
2020-08-21 | GSE148755 | GEO
Project description:Sacharomyces cerevisiae Transcript Isoform mapping (set2)
| PRJNA488283 | ENA
Project description:Isoform switching events in esophageal adenocarcinoma progression
| PRJNA798444 | ENA
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.
2022-08-17 | GSE193946 | GEO
Project description:Characterization of splice isoform switching during human kidney development
| PRJNA633147 | ENA
Project description:Zebrafish embryos are transcriptional silent until activation of the zygotic genome during the 10th cell cycle. Onset of transcription is followed by cellular and morphological changes involving cell speciation and gastrulation. Previous genome-wide surveys of transcriptional changes only assessed gene expression levels; however, recent studies have shown the necessity to map isoform-specific transcriptional changes. Here we perform isoform discovery and quantification on transcriptome sequences from before and after zebrafish zygotic genome activation (ZGA). We identify novel isoforms and isoform switches during ZGA for genes related to cell adhesion, pluripotency and DNA methylation. Isoform switching events include alternative splicing and changes in transcriptional start sites and in 3’ untranslated regions. New isoforms are identified even for well-characterized genes such as pou5f1, sall4 and dnmt1. Genes involved in cell-cell interactions such as f11r and magi1 display isoform switches with alterations of coding sequences. We also detect over 1000 transcripts that acquire a longer 3’ terminal exon when transcribed zygotically relative to the maternal transcript counterparts. ChIP-seq data mapped onto skipped exon events reveals a correlation between histone H3K36trimethylation peaks and the skipped exons, suggesting epigenetic marks being part of alternative splicing regulation. The novel isoforms and isoform switches reported here include regulators of the transcriptional, cellular and morphological changes taking place around ZGA. Our data display an array of isoform-related functional changes and represent a valuable resource complementary to existing early embryo transcriptomes. Examination H3K36me3 in zebrafish whole embryos at the Post-MBT stage
2012-11-01 | E-GEOD-40629 | biostudies-arrayexpress