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Gene expression and intron retention analysis of bktRNA1-depleted human cells

ABSTRACT: Backwark kink-turn RNA 1 (bktRNA1) is a novel post-transcriptional regulator with a role in RNA modification. Here, we show that human bktRNA1 interacts with 15.5K and FBL and guides 2’-O-methylation in the 8th of U12 snRNA. Given that U12 plays crucial role in minor intron splicin, we knockouted bktRNA1 in HCT116 cells and examined the effects of the modification on minor splicing by transcriptome analyses. Our work defines a novel functional interaction bwtween bktRNA1 and RNA processing and highlighs that a single modification alteration may contribute to global impairment of the splicing machinery.

ORGANISM(S): Homo sapiens

PROVIDER: GSE160515 | GEO | 2023/04/10

REPOSITORIES: GEO

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Gene expression and intron retention analysis of 15.5K-knockdown human cells

Project description:15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in gene expression and intron retention.

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Genome-wide analysis of gene expression and intron retention during deveopment in a U12-type splicing-deficient zebrafish mutant [microarray]

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2014-02-05 | E-GEOD-53934 | biostudies-arrayexpress

Genome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant [RNA-seq]

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Genome-wide analysis of gene expression and intron retention during deveopment in a U12-type splicing-deficient zebrafish mutant [microarray]

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Genome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant [RNA-seq]

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CLASH for 15.5K and FBL proteins in HEK293T cells

Project description:We performed CLASH for 15.5K and FBL in HEK293T cells which overexpressed 15.5K and FBL, respectively.

2023-04-10 | GSE160636 | GEO

SMN deficiency in spinal muscular atrophy causes widespread intron retention and DNA damage

Project description:Spinal muscular atrophy is the leading genetic cause of infant mortality and is caused by homozygous loss of the SMN1 gene. We investigated global transcriptome changes in the spinal cord of inducible SMA mice. SMN depletion caused widespread retention of introns with weak splice sites or belonging to the minor (U12) class. We further demonstrated accumulation of DNA double strand breaks in the spinal cord of SMA mice and in human SMA cell culture models. DNA damage was partially rescued by suppressing the formation of R-loops, which accumulated over retained introns. We propose that instead of single gene effects, pervasive splicing defects caused by SMN deficiency trigger a global DNA damage and stress response, thus compromising motor neuron survival.

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Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition.

Project description:Most metazoans contain two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which recognizes <1% of introns. Despite their rarity, minor introns are exquisitely conserved amongst species, suggesting important regulatory functions. However, physiologic roles for the minor spliceosome and the relevance of recurrent, leukemia-associated mutations affecting minor spliceosome components are not well understood. Here, we identify that mutational loss of the minor spliceosomal factor ZRSR2 enhances hematopoietic stem cell self-renewal via impaired minor intron splicing that converges on LZTR1, a regulator of Ras-related GTPases. LZTR1 minor intron retention is additionally observed in Noonan syndrome and diverse cancers. These data uncover minor intron recognition as a regulator of hematopoiesis and mechanistic links between ZRSR2 mutations, LZTR1, and leukemia.

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Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition

Project description:Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles for the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections between minor introns, hematopoiesis, and cancers are unclear. Here, we identify that impaired minor intron excision via ZRSR2 loss enhances hematopoietic stem cell self-renewal. CRISPR screens mimicking nonsense-mediated decay of minor intron-containing mRNAs converged on LZTR1, a regulator of Ras-related GTPases. LZTR1 minor intron retention was also discovered in the RASopathy Noonan syndrome, due to intronic mutations disrupting splicing, and diverse solid tumors. These data uncover minor intron recognition as a regulator of hematopoiesis, noncoding mutations within minor introns as cancer drivers, and links between ZRSR2 mutations, LZTR1 regulation, and leukemias.

2021-02-09 | GSE149455 | GEO

CRISPR-Cas9 knockdown of RBM48 in K562 cells

Project description:U12-type or minor (U12) introns are spliced by a distinct minor spliceosome and are found in the vast majority of multicellular eukaryotes, including plants and animals. Although U12 introns constitute less than 0.5% of all introns in many species, minor intron containing genes (MIGs) are important for organismal growth, development and pathology. We recently reported that maize RNA Binding Motif Protein 48 (RBM48) is required for U12-type intron splicing. Maize rbm48 mutants have genome-wide defects of U12 intron splicing, leading to abnormal endosperm cell differentiation and proliferation. To investigate whether RBM48 mediated U12 splicing is conserved between maize and humans, we generated a CRISPR/Cas9-mediated RBM48 functional knockout of the human RBM48 ortholog (RBM48 FunKO) in human K-562 cells.

2020-08-20 | GSE156471 | GEO

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