Project description:Tri-methylation of histone H3 lysine 27 is catalyzed by Polycomb Repressive Complex 2 (PRC2). By genome-wide mapping of H3K27me3 sites in HEK293 cells, we are able to identify potential sites for PRC1-mediated repression and use these data to inform gene expression experiments in the presence and absence of pharmacological inhibition or KD/KO of various Polycomb subunits.
Project description:The Yin Yang 2 (YY2) gene encodes a zinc finger transcription factor that is not well characterized, yet. By using chromatin immunoprecipitations combined with whole-genome human promoter microarray (ChIP-chip) in HEK293 cells, we identified a multiplicity of YY2-bound annotated promoters as well as additional chromosomal regions. Interestingly, gene ontology analyses linked YY2 to fundamental biological pathways associated to cancer and developmental processes. Identification of YY2 target genes in HEK293 cells in vivo
Project description:H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we utilized hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are enriched or depleted for H2A.Z. Mass spectrometry measurement of histone protein abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robust global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.
Project description:Polycomb group (PcG) proteins including EZH2, SUZ12 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes. To completely understand the epigenetic profile and molecular network of PcG in HCC, we performed ChIP-on-chip screens with EZH2, SUZ12 and H3K27me3 antibodies in HepG2 cells. Comparison of ChIP-on-chip results from EZH2, SUZ12 and H3K27me3.
Project description:We report the genomic occupancy of the BAHD1 protein in HEK293 cells over-expressing the BAHD1 gene (HEK293-HPT-BAHD1) We used Native ChIP-seq to identify DNA regions bound to BAHD1 (native ChIP involves use of native chromatin before precipitation of immune complexes, without formaldehyde crosslinking of proteins with nucleic acids)
Project description:The Yin Yang 2 (YY2) gene encodes a zinc finger transcription factor that is not well characterized, yet. By using chromatin immunoprecipitations combined with whole-genome human promoter microarray (ChIP-chip) in HEK293 cells, we identified a multiplicity of YY2-bound annotated promoters as well as additional chromosomal regions. Interestingly, gene ontology analyses linked YY2 to fundamental biological pathways associated to cancer and developmental processes.