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TranscriptomicsA single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast
Mammalian SR proteins are a family of reversibly phosphorylated RNA binding proteins primarily studied for their roles in alternative splicing. While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been primarily studied for the...
ORGANISM(S): Saccharomyces cerevisiae 
2008-12-30 | E-GEOD-11491 | biostudies-arrayexpress
TranscriptomicsRegulation of alternative splicing by histone modifications
Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. Here, we demonstrate a direct role for histone modifications in alternative splicing. We find distinctive histone modification signatures which correlate with splicing ou...
ORGANISM(S): Homo sapiens 
2010-02-10 | E-GEOD-19373 | biostudies-arrayexpress
TranscriptomicsKnockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA
Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical s...
ORGANISM(S): Mus musculus 
2016-03-07 | E-GEOD-69733 | biostudies-arrayexpress
GenomicsSF3B1 association with chromatin determines splicing outcomes
Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. Part of the explanation probably lies in differences in chromatin organization between exons and introns. Pro...
ORGANISM(S): Homo sapiens 
2015-04-22 | E-GEOD-65644 | biostudies-arrayexpress
TranscriptomicsRegulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery (RNA-Seq)
Protein Arginine MethylTransferase 5 (PRMT5) is known to mediate epigenetic control on chromatin and to functionally regulate components of the splicing machinery. In this study we show that selective deletion of PRMT5 in different organs leads to cell cycle arrest and apoptosis. At the molecular le...
ORGANISM(S): Mus musculus 
2013-09-13 | E-GEOD-45284 | biostudies-arrayexpress
TranscriptomicsMisregulation of alternative splicing of BIN1 leads to T-tubule alterations and muscle weakness in myotonic dystrophy
Myotonic dystrophes (DM), the most common adult muscular dystrophy, are the first recognized examples of RNA-mediated diseases in which expression of mutant RNAs containing expanded CUG or CCUG repeats interfere with the splicing of other mRNAs. Using whole-genome microarrays, we found that alternat...
ORGANISM(S): Homo sapiens 
2011-05-26 | E-GEOD-21795 | biostudies-arrayexpress
TranscriptomicsMADS: a New and Improved Method for Analysis of Differential Alternative Splicing by Exon-tiling Microarrays
We describe a method, MADS (Microarray Analysis of Differential Splicing), for discovery of differential alternative splicing from exon tiling microarrays. MADS incorporates a series of low-level analysis algorithms motivated by the “probe-rich” design of exon arrays, including background correction...
ORGANISM(S): Mus musculus 
2008-05-09 | E-GEOD-11344 | biostudies-arrayexpress
Genomicsm6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover
m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover
PRJNA341466 | ENA
GenomicsTCERG1 regulates alternative splicing of Bcl-x gene by modulating the rate of RNAPII transcription
Complex functional coupling exists between transcriptional elongation and pre-mRNA alternative splicing. Pausing sites and changes in the rate of transcription by RNAPII may therefore have a fundamental impact in the regulation of alternative splicing. Here, we show that the elongation and splicing-...
ORGANISM(S): Homo sapiens 
2012-01-12 | E-GEOD-33716 | biostudies-arrayexpress
TranscriptomicsSplicing function of mitotic regulators links R-loop mediated DNA damage to tumor cell killing
We discovered that two mitotic regulators, BuGZ and Bub3, involved in splicing regulation during interphase 8 samples from primary Human foreskin fibroblast cells (HFFs) , 12 samples from TOV21G cells. Control siRNA. BuGZ siRNA or Bub3 siRNA were transfected for 48 h before sample collection. Cells ...
ORGANISM(S): Homo sapiens 
2015-04-11 | E-GEOD-67770 | biostudies-arrayexpress
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