Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [NTD-Seq]
Ontology highlight
ABSTRACT: 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
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
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
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.
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
Project description:To investigate changes in the elongating form of RNA Polymerase II across different conditions, we peformed ChIP-seq using antibody against the Ser2P RNAPII of pTEFb in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP and Input fractions to investigate Ser2P RNAPII distribution changes
Project description:To investigate changes in the elongating form of RNA Polymerase II across different conditions, we peformed ChIP-seq using antibody against the Ser5P RNAPII of pTEFb in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP and Input fractions to investigate Ser5P RNAPII distribution changes
Project description:To investigate changes in the histone marks and RNA Polymerase II across different conditions, we peformed CUT&RUN seq using antibody against H3K4me3, H3K27me3, H3K27ac, and H3K4me1 in K562 cells at 4 days after modified allele expression, or H3K4me3 and Ser2P RNAPII in human CD34 cells We then performed coverage plot analyses using data obtained from CUT&RUN to investigate changes in histone marks or Ser2P RNAPII
Project description:To investigate changes in the H3K36me3 distribution across different conditions, we peformed ChIP-seq using antibody against the H3K36me3 in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP fractions to investigate H3K36me3 distribution changes
Project description:To investigate changes in the CHD1 distribution across different conditions, we peformed ChIP-seq using antibody against the CHD1 in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP fractions to investigate CHD1 distribution changes
Project description:To investigate changes in the INTS-11 distribution across different conditions, we peformed ChIP-seq using antibody against INTS11 in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP fractions to investigate INTS11 distribution changes