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U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs (ChIP-Seq)

ABSTRACT: RNAPII ChIP-seq analysis in U2 and U6 antisense morpholino oligonucleotide (AMO)-treated HeLa cells in comparison to negative control (NC) AMO To investigate if U2 or U6 AMO treatment caused transcription defect, we carried out RNAPII ChIP-seq analysis in control, U2 and U6 AMO treated HeLa cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE250343 | GEO | 2025/01/29

REPOSITORIES: GEO

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U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs (RNA-Seq)

Project description:To investigate the extent to which U6 AMO affects transcriptome. we performed mRNA-seq in control, U1 and U6-AMO treated sample

2025-01-29 | GSE250344 | GEO

U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs (3'-Seq)

Project description:To investigate the extent to which U6 inhibits premature cleavage and polyadenylation at the transcriptome level. we performed 3’-seq in control, U1 and U6-AMO treated sample using lexogen 3’-seq kit (Cat. 016.24) that could accurately quantify the global PAS usage. Indeed, we found both U1 and U6 could globally suppress intronic PCPA.

2025-01-29 | GSE250342 | GEO

U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs

Project description:U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs

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U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [ChIP-seq]

Project description:To understand how U4 snRNP regulates premature cleavage and polyadenylation of pre-mRNAs at the transcriptome wide, we conducted RNAPII ChIP-seq analysis on control, U1 and U4-AMO treated samples.

2024-06-26 | GSE262384 | GEO

U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [mRNA-seq]

Project description:To understand how U4 snRNP regulates premature cleavage and polyadenylation of pre-mRNAs at the transcriptome wide, we conducted mRNA-seq analysis on control, U1 and U4-AMO treated HeLa cells

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mRNA 3'-seq analysis in NIH3T3 cells treated with different concentration of negative control (NC) and U1/U4/U6/U2 AMOs（0.05, 0.5, 10 uM)

Project description:To understand if U1/U6/U4/U2 snRNPs could regulate 3'-UTR APA, we treated NIH3T3 cells with different concentration of U1/U6/U4/U2 AMOs

2025-01-29 | GSE283688 | GEO

U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-01-27 | GSE250345 | GEO

RiboMeth-Seq analysis of purified U6 and U2 snRNAs

Project description:The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. To investigate the relevance of this interaction, U6 or U2 snRNAs were purified from total RNA by pulldown of biotinylated antisense oligonucleotides and the occurence of 2’-O-methylations was investigated by RiboMeth-seq analysis. A comparison between U6 and U2 snRNA isolated from HEK293 wildtype or LARP7 knockout cell lines revealed that 2’-O-methylations of the U6 snRNA are specifically lost in the absence of LARP7. Alazami syndrome is a form of primary dwarfism associated with mutations in the LARP7 gene. RiboMeth-seq analyses performed with RNA isolated from blood samples of two Alazami patients or healthy parents as well as from B-lymphoblastoid cell lines (B-LCLs) derived from an Alazami patient and from a healthy parent confirmed the impact of mutant LARP7 protein variants on the 2’-O-methylation profile of the U6 snRNA.

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Transcriptome changes in splicing inhibited cells

Project description:In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. This did not occur when splicing was inhibited with U2 snRNA antisense morpholino oligonucleotide or the U2-snRNP-inactivating drug spliceostatin A unless U1 antisense morpholino oligonucleotide was also included. We further show that U1 snRNA–pre-mRNA base pairing was required to suppress premature cleavage and polyadenylation from nearby cryptic polyadenylation signals located in introns. These findings reveal a critical splicing-independent function for U1 snRNP in protecting the transcriptome, which we propose explains its overabundance.

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RiboMeth-Seq analysis of purified U6 and U2 snRNAs

Project description:RiboMeth-Seq analysis of purified U6 and U2 snRNAs

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