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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [nascent RNAseq]

ABSTRACT: As a complementary approach to GROseq, we peformed short read sequencing of nascent RNA (nSRS-seq) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed nascent gene transcription expression using data obtained from nSRS-seq

ORGANISM(S): Homo sapiens

PROVIDER: GSE226000 | GEO | 2024/03/12

REPOSITORIES: GEO

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [GRO-seq]

Project description:To investigate redistribution of RNAPII in response to the SF3B1 mutation and to study its effects on nascent gene expression, we peformed fastGRO-seq (variant of GRO-seq using 4-thio-UTP based nuclear run-on) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed metaplot-based and gene expression analysis using data obtained from fastGRO-seq

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Long read sequencing]

Project description:To understand how SF3B1K700E impacts co-transcriptional splicing, we peformed long read sequencing of RNA (nSRS-seq) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed co-transcriptional splicing efficiency analysis using data obtained from Long read sequencing

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [DRIP-seq]

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [RNA-seq]

Project description:To investigate the impact of altered transcription and chromatin on steady state transcript levels, we peformed gene expression and splicing analysis in K562 cells (wild type and SF3B1K700E mutant) at 4 and 8 days after mutant allele expression We then performed gene expression profiling analysis using data obtained from RNA-seq at two time points.

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [NTD-chIP-seq]

Project description:To investigate changes in RNAPII distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against N-terminal domain of RNAPII (Pan-Pol2) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed coverage plot analysis using data obtained from ChIP-seq to investigate RNAPII distribution changes

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Disruption of RNAPII transcription elongation links Oncogenic SFB31 mutations to replciation stress and targetable alterations in chromatin landscape [mNET-Seq]

Project description:To investigate changes in RNAPII distribution in response to SF3B1 mutations, we peformed mNET-seq using antibody against either pan Pol II CTD or Ser2P Pol II CTD in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed coverage plot analysis using data obtained from mNET-seq to investigate RNAPII distribution changes. Drosophila spike-in was included for the pan-Pol II CTD studies.

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [TT-TL seq]

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Murine ChIP-Seq]

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