Hspb1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43979 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Recon 2M.2 is a generic genome-scale metabolic model of Homo sapiens, in which a framework for gene-transcript-protein-reaction associations (GeTPRA) was deployed to generate metabolic reactions by considering the effects of alternative splicing of metabolic genes (i.e., both principal and non-principal transcripts). Eight versions of COBRA-compliant SBML files are available for Recon 2M.2 depending on the use of: MNXref versus BiGG IDs (metabolite IDs); Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).
2022-05-16 | MODEL2205110002 | BioModels
Project description:Mutations of the RNA-granule component TDRD7 (OMIM: 611258) cause pediatric cataract in humans. Here, we applied an integrated approach to elucidate the molecular pathology of cataract in Tdrd7 targeted-knockout (Tdrd7-/-) mice. Tdrd7-/- animals precipitously develop lens fiber cell abnormalities early in life, suggesting a global-level breakdown/mis-regulation of key cellular processes. High-throughput RNA-sequencing followed by iSyTE-integrated bioinformatics-based analysis identified the molecular chaperone and cytoskeletal-modulator, HSPB1 (HSP27), among the high-priority down-regulated candidates in Tdrd7-/- lens. Moreover, a protein 2-D fluorescence difference gel electrophoresis-coupled mass spectrometry screen also identified HSPB1 to be reduced in Tdrd7-/- lens, offering independent support for focusing efforts on this factor to explain Tdrd7-/- cataract. Reduction of HSPB1 preceded lens morphological abnormalities, suggesting that cytoskeletal defects underlie the Tdrd7-/- cataract phenotype. In agreement, scanning electron microscopy revealed abnormal fiber cell membrane protrusions in Tdrd7-/- lenses. Significantly, abnormal F-actin staining was detected specifically in Tdrd7-/- fiber cells that exhibit nuclear degradation, thereby revealing that there are distinct mechanisms based on pre- or post-nuclear degradation differentiation stage for F-actin cytoskeletal maintenance in fiber cells. Further, RNA-immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA-imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in a specific pre-nuclear degradation area of differentiating fiber cells, indicating that TDRD7-ribonucleoprotein complexes are necessary for controlling optimal levels of key factors in lens development. Together, these data uncover a novel role for TDRD7 in regulating elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.
2020-09-01 | GSE134384 | GEO
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.
2011-06-07 | GSE23525 | GEO
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:Analysis of the maize alternative splicing landscape, including transcript discovery and mapping of genotype-dependent variations in alternative splicing using B73, Mo17 and the SX19 inbred mapping population
2014-10-29 | GSE57337 | GEO
Project description:Transcript shortening through alternative polyadenylation promotes gene expression during fracture healing
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Project description:Landscape of ribosome-engaged alternative transcript isoforms across neuronal cell classes
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Project description:Purpose: Identify alternative splicing events and changes to transcript expression levels
2022-07-05 | GSE182779 | GEO