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

ABSTRACT: To investigate changes in chromatin landscape and nucleosome positioning in response to SF3B1 mutations, we peformed ATAC seq in K562, human CD34, and murine cKit+,Sca1+,Lin- cells We then performed peak-based and nucleosome positioning analyses using data obtained from ATAC to investigate changes in chromatin accessibility and promoter nucleosome occupancy, respectively

ORGANISM(S): Homo sapiens

PROVIDER: GSE254795 | 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 [ATAC-seq]

Project description:To investigate changes in chromatin landscape and nucleosome positioning in response to SF3B1 mutations, we peformed ATAC seq in K562, human CD34, and murine cKit+,Sca1+,Lin- cells We then performed peak-based and nucleosome positioning analyses using data obtained from ATAC to investigate changes in chromatin accessibility and promoter nucleosome occupancy, respectively

2024-03-12 | GSE225993 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [NTD-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 We then performed coverage plot analysis using data obtained from ChIP-seq to investigate RNAPII distribution changes

2024-03-12 | GSE254796 | GEO

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

Project description:To investigate changes in Pol2 distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against Pol2 (both CTD and elongation specific (Ser2P and Ser5p). For the murine model, SF3B1 mutant (and WT counterparts) were treated with tamoxifen daily x 5 days at 5 weeks of age. Mice were euthanized at end of week 7 and bone marrow was harvested to isolate lineage negative cells We then performed coverage plot analysis using data obtained from ChIP-seq from IP fractions to investigate Pol2 distribution changes

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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

2024-03-12 | GSE225997 | GEO

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 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 [CDK9-chIP-seq]

Project description:To investigate changes in p-TEFb distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against the CDK9 component of pTEFb 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 from IP and Input fractions to investigate CDK9 distribution changes

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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]

Project description: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

2024-03-12 | GSE226000 | GEO

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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2024-03-12 | GSE226001 | GEO

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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