Project description:We investigated SOX18 binding events on the chromatin under basal conditions in human umbilical vein endothelial cells, upon overexpression of mouse Sox18-cMyc and immunoprecipitating cMyc. Cells overexpressing only the cMyc tag were used as negative control condition, and peaks called here were substracted from the Sox18-cMyc peaks.
Project description:The experiment was designed to identify differential gene expression due to dominant negative mutation of the Sox18 gene in the ragged Opossum spontaneous mouse mutant. Gene expression was analysed after whole RNA isolation in dermal spheres as hair follicle inductive mesenchyme tissue, and was intended to identify gene expression patterns associated with alteration of hair induction post Sox18 mutation.
Project description:We investigated SOX7 binding events on the chromatin under basal conditions in human umbilical vein endothelial cells, upon overexpression of human SOX7-mCherry and immunoprecipitating mCherry. Cells overexpressing only the mCherry tag were used as negative control condition, and peaks called here were substracted from the SOX7-mCherry peaks.
Project description:While the core members of the Polycomb family of proteins (PRC2, PRC1, PR-DUB) are well-characterized, little is known about the specific composition of and protein-protein interactions within these complexes in different cell types. We performed quantitative interaction proteomics and cross-linking mass spectrometry on core Polycomb complex members to identify novel interactors, the relative abundance (stoichiometry) of subunits, and the architecture of these complexes in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). Differentiation to NPCs resulted in dramatic binding changes for several substoichiometric interactors of PRC2 and PRC1. ChIP-seq of core PRC2 and PRC1 subunits in mESCs and NPCs also identified dynamic changes in the genomic localization of these complexes. We observed a loss of PRC2 from most H3K27me3 sites during differentiation, whereas PRC1 is retained at these sites. Additionally, we found PRC1 at enhancers and promoters of active genes independent of PRC2 binding. Overexpression studies using NPC-specific PRC1 interactors demonstrated that the subunit switching observed during differentiation can change PRC1 target site binding. Altogether, these findings extend our understanding of Polycomb family composition, architecture, and genome-wide localization. ChIP-seq samples for Suz12, Ezh2, Ring1b, Pcgf2, and inputs from mouse embryonic stems cells (mES) and neural progenitor cells (NPC) as well as NPC histone H3K4me1 ChIP-seq.
Project description:PRDM9 is a histone methyltransferase expressed in meiotic germ cells that determines the location of genetic recombination hotspots through binding of its allele-specific DNA binding domain. Here we characterize the genome-wide chromatin modification for two human PRDM9 alleles (A and C) in human cell lines. HEK293 cells were transfected with both alleles and an empty vector control. Resulting chromatin was subjected to H3K4me3 ChIP followed by high-throughput sequencing. We find that different PRDM9 allele largely modified chromatin in entirely different genomic regions in somatic cells determined by the protein's zinc-finger DNA binding domains. Many of the allele-specific peaks overlap sites of meiotic double-strand breaks found in vivo in human germ cells suggesting that transient expression of PRDM9 in somatic cells can reflect binding in vivo. Identify PRDM9-dependent H3K4me3 sites by comparing modified chromatin after expression of different human PRDM9 alleles in HEK293 cells.
Project description:The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. ChIP-Seq in Beta-TC6 mouse beta cells
Project description:Three transcription factors KLF5, GATA4 and GATA6 are recurrently amplified in multiple gastric cancer cohorts, representing one type of lineage-survival oncogenes in gastric cancer. ChIP-Seq analysis of these three factors in multiple cell lines revealed that significant number of genomic sites are co-occupied by KLF5 and GATA4 and/or GATA6. Integrative analysis of ChIP-Seq and gene expression identified several targets of the three transcription factors in both cell lines and primary tumors, including HNF4A. These results suggest that KLF5, GATA4 and GATA6 interact and co-operate to regulate HNF4A and other genes to promote tumorigenesis in gastric cancer. ChIP-Seq experiments of KLF5, GATA4 and GATA6 were performed in three gastric cancer cell lines YCC3, AGS and KATOIII
Project description:The Crown-of-thorns starfish (COTS) Acanthaster planci feeds on hard corals and its outbreaks are a major cause of destruction of coral communities on the Australian Great Barrier Reef. Whilst population booms and the social behaviour of COTS have been well studied, little is known about the neural mechanisms underlying COTS metabolism and behaviour. One of the major classes of chemical messengers that regulate metabolic and behavioural processes in animals are neuropeptides. Here, we have analysed COTS genome and transcriptome sequence data to identify neuropeptide precursor proteins in this species. Mass spectrometry was employed to identify neuropeptides extracted from radial nerve cords. Forty-nine neuropeptide precursors were identified, including homologs of neuropeptide signaling systems that are evolutionarily conserved throughout the Bilateria.
Project description:Using ChIP-seq for p300 and H3K4me1, we identified 2,489 putative melanocyte enhancer loci in the mouse genome. We demonstrated that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression with high frequency in cultured melanocytes and in melanocytes of transgenic zebrafish. ChIP-seq for EP300 and H3K4me1 in the mouse melanocyte cell line melan-a.
Project description:Study of Sox18 regulated genes: Human umbilical vein endothelial cells (HUVEC) were either transduced with adenoviral vectors expressing SOX18 from an IRES-EGFP casette, or IRES-EGFP alone, or left untreated. After 16 hours, mRNA was isolated and analyzed by hybridization to Affymetrix HG-U133A arrays. Overall design: Human umbilical vein endothelial cells (HUVEC) were either transduced with adenoviral vectors expressing SOX18 from an IRES-EGFP casette, or IRES-EGFP alone, or left untreated. After 16 hours, mRNA was isolated and analyzed by hybridization to Affymetrix HG-U133A arrays.