RNA-seq experiments from Saccharomyces cerevisiae overexpressing ubiquitin-related protein Hub1
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE84215 | GEO | 2017/06/01
SECONDARY ACCESSION(S): PRJNA328390
REPOSITORIES: GEO
Similar Datasets
Project description:The conserved ubiquitin-like protein Hub1/UBL-5 associates with proteins non-covalently. In yeast and human cells, Hub1 promotes splicing of precursor mRNAs with weak introns and alternative splicing, however, its splicing function has remained elusive in multicellular organisms. We demonstrate the splicing function of Hub1/UBL-5 in the free-living nematode Caenorhabditis elegans. UBL-5 binds to the HIND-containing splicing factors Snu66/SART-1 and PRP-38 and associates with other spliceosomal proteins. Caenorhabditis elegans hub1/ubl-5 mutants die at the larval L3 stage, and show accumulation of intron- and outron-containing transcripts. The latter observation adds to UBL-5’s splicing function in trans-RNA splicing. UBL-5 complements splicing defects of hub1-knockout Schizosaccharomyces pombe, confirming its functional conservation. Thus, UBL-5 is important for C. elegans development and cis- and trans-RNA splicing.
2024-05-21 | PXD033914 | Pride
Project description:Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast, however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing.
2014-05-30 | GSE56878 | GEO
Project description:Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast, however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing. Human U2OS cells were transfected with siRNAs to specifically knockdown the ubiquitn-like protein Hub1. Cells treated with non-targeting oligos (GL2) served as negative control. Total RNAs of three biological replicates of each knockdown experiment were isolated and changes of splicing patterns were subsequently analyzed by Affymetrix GeneChip Human Exon 1.0 ST arrays
2014-05-30 | E-GEOD-56878 | biostudies-arrayexpress
Project description:RNA-seq experiments from Saccharomyces cerevisiae overexpressing ubiquitin-related protein Hub1
| PRJNA328390 | ENA
Project description:Bacillus cereus HuB1-1 Genome sequencing
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Project description:HISTONE MONOUBIQUITINATION1 (HUB1) and its ortholog HUB2 regulate expression of genes involved in flowering, dormancy and circadian clock. HUB1 and HUB2 interact with two RNA-binding proteins KHD and SPEN. Phenotype analysis of the knock-down khd1-1, knock-out spen3-1, and knock-out hub mutants suggested that KHD and SPEN may contribute to flowering- and circadian clock-related functions that are also target of HUB1/2 activity. Transcriptome analysis was performed using RNA extracted from shoot apices of 10-day-old seedlings. After library preparation by TruSeq, RNA was sequenced on the Illumina HiSeq.
2018-05-14 | E-MTAB-6780 | biostudies-arrayexpress
Project description:Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs. We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron. We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast.
2016-08-01 | GSE68022 | GEO
Project description:au10-03_hub1 - kinetics of gene expression after light exposure in hub1-3 mutant compared to wild-type - Role of histone UbH2B in the regulation of gene expression in response to light - RNA from 5-day-old wild-type and hub1-3plants in 3 conditions were used for hybridization: 5 days of darkness, 5 days of darkness + 1 hour of light and 5 days of darkness + 6 hours of light. Keywords: genotype comparaison,time course
2011-05-20 | GSE21922 | GEO
Project description:Sites of ubiquitin modification have been identified by mass spectrometry based on the increase in molecular mass of a tryptic peptide carrying two additional glycine residues from the ubiquitin moiety. However, such peptides with GG shifts have been difficult to discover. We identify 870 unique sites of ubiquitin attachment on 438 different proteins of the yeast Saccharomyces cerevisiae.
| S-EPMC3337332 | biostudies-literature
Project description:In the yeast Saccharomyces cerevisiae the TOR complex 1 (TORC1) controls many growth-related cellular processes and is essential for cell growth and proliferation. Macrolide antibiotic rapamycin, in complex with a cytosol protein named FKBP12, specifically inhibits TORC1, causing growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FRB domain of the TOR proteins. In an attempt to understand the role of the FRB domain in TOR function, we identified a single point mutation (Tor2(W2041R) ) in the FRB domain of Tor2 that renders yeast cells rapamycin resistant and temperature sensitive. At the permissive temperature, the Tor2 mutant protein is partially defective for binding with Kog1 and TORC1 is impaired for membrane association. At the restrictive temperature, Kog1 but not the Tor2 mutant protein, is rapidly degraded. Overexpression of ubiquitin stabilizes Kog1 and suppresses the growth defect associated with the tor2 mutant at the nonpremissive temperature. We find that ubiquitin binds non-covalently to Kog1, prevents Kog1 from degradation and stabilizes TORC1. Our data reveal a unique role for ubiquitin in regulation of TORC1 and suggest that Kog1 requires association with the Tor proteins for stabilization.
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