Comparision of Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II binding on Hox and non-Hox genes
ABSTRACT: Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II binding pattern in WT and Psip1 KO MEFs Menin occupancy is studied over Hox genes and several non-hox genes Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II ChIPs from WT and Psip1 KO MEFs
Project description:Psip1/p75 binds to Hox genes and colocalizes with Mll1 and in Psip1 KO MEFs Mll1 occupancy is reduced over Hox genes Psip1/p75 ChIP using A300-848 abtibody (recognises p75 isoform of Psip1) and Mll1 ChIP from WT and Psip1 KO MEFs ChIP-chip
Project description:The p52 isoform of Psip1/Ledgf links histone H3K36 methylation and the regulation of alternative splicing. Chromatin immunoprecipitation (ChIP) of Psip1 together with H3K36me3 and Srsf1 and by ChIP-on-chip analysis demonstrated that H3K36me3, Psip1 and SRSF1 enrichment correlates on the gene bodies Array design includes 2 dye swap replicates for Srsf1 and Psip1-/- samples, and single arrays for PSIP and H3K36me3 samples
Project description:The p52 isoform of Psip1/Ledgf links histone H3K36 methylation and the regulation of alternative splicing. Chromatin immunoprecipitation (ChIP) of Psip1 together with H3K36me3 and H3K4me3 and by ChIP-on-chip analysis demonstrated that, Like H3K36me3, Psip1 is enriched on exons of highly expressed genes, Comparision of H3K36me3 and Psip1 binding sites on the expressed and non expressed genes.
Project description:We profiled the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II following mitogen stimulation. We classified the genes that rapidly coassemble p300 and pol II following mitogen stimulation Comparison the unstimulated to P/I stimulated pol II and p300 enrichment fold in Jurkat
Project description:Using pol II mutants in human cells we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; H3K36me3 shifted within genes toward 5’ ends and H3K4me2 extended further upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5’ ends of genes that is conserved in yeast. We propose a “dwell-time in the target zone” model to explain the effects of transcriptional dynamics on establishment of co-transcriptionally deposited protein modifications. Promoter-proximal Ser2 phosphorylation is associated with longer pol II dwell time at start sites and reduced transcriptional polarity due to strongly enhanced divergent antisense transcription at promoters. Overall design: The effect of transcription elongation rate on histone H3K36me3, H3K4me2 and pol II CTD phosphorylation was analyzed by ChIP-seq in isogenic human HEK293 cell lines that inducibly express a-amanitin resistant mutants of the RNA polymerase II large subunit with slow elongation rates. Anti-pol II total nascent RNA sequencing (tNET-seq) was developed to assay transcription by WT and slow pol II. Slow pol II mutants in S. cerevisiae were also assayed for pol II CTD Ser2 phosphorylation.
Project description:Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of Ser-5-phosphorylated RNA polymerase II and Ser-2-phosphorylated RNA polymerase II in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the increase of the initiating form of RNA polymerase II (Ser5-phosphorylated) and in the aberrant loss of the elongating form of RNA polymerase II (Ser2-phosphorylated) of pluripotency genes in ESCs. Overall design: Ten million cells were used for the ChIP and precipitated using 10 micrograms of antibody against Ser-5-Phosphoryalted RNA polymerase II (Abcam, ab5131 ) and against Ser-2-Phosphoryalted RNA polymerase II (Active Motif, clone 3E10)
Project description:We study the impact of inhibiting Pol II-Se2 phosphorylation on Pol II binding and histone modifications in the mouse T cell line P5424. Overall design: Genome-wide analysis via ChIP-Seq for total RNA Pol II binding, H3K4me1, H3K4me2 and H3K4me3 in murine P5424 cells with tow conditions: KM05283 treatment (Inhibitor of Pol II Ser2 phosphorylation) or control DMSO.