Project description:We investigate the aging changes for Histone marks H3K4me3, H3K27me3 and H3K36me3 for mouse hematopoietic stem cells. Mouse hematopoietic stem cell histone methylation profiles of 4 month and 24month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000
Project description:We investigate the dynamics for Histone marks H3K4me3 and H3K27me3 during Dnmt3a and Dnmt3b knockout in mouse hematopoietic stem cells. The term dko represents double knockout of both Dnmt3a and Dnmt3b, while the term sko denotes single knockout of Dnmt3a. The Wildtype profiles were generated in study GSE47765. Mouse hematopoietic stem cell histone methylation profiles of sko and dko mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000
Project description:Canonical Wnt signalling regulates the self-renewal of most if not all stem cell systems. In the blood system, the role of Wnt signalling has been subject of much debate, with positive and negative roles of Wnt signalling proposed for hematopoietic stem cells (HSC). As we have shown previously, this controversy can be largely explained by the effects of different dosages of Wnt signalling. What remained unclear however, was why high Wnt signals would lead to loss of reconstituting capacity. To better understand this phenomenon, we have taken advantage of a series of hypomorphic mutant Apc alleles resulting in a broad range of Wnt dosages in HSCs, purified those HSCs and performed whole genome gene expression analyses. Gene expression profiling and functional studies show that HSCs with APC mutations lead to high Wnt levels , enhanced differentiation and diminished proliferation, but have no effect on apoptosis, collectively leading to loss of stemness. Thus, we provide mechanistic insight into the role of APC mutations and Wnt signalling in HSC biology. As Wnt signals are explored in various in vivo and ex vivo expansion protocols for HSCs, our findings also have clinical ramifications. To investigate the effects of Wnt signals in hematopoietic cells, mice carrying floxed Apc or hypomorphic Apc mutants were crossed, LSK cells were isolated and treated with Cre IRES GFP gamma-retrovirus ex vivo, GFP+ cells were sorted and RNA expression was determined.
Project description:Human cSki was overexpressed using MIGR1 retrovirus in sorted murine Lin-c-Kit+Sca-1+ cells. Cells were infected and cultured for 2 days after infection prior to isolation of GFP+ve cells and microarray. GFP+ve MIGR1 and cSKI cells were compared. Each sample represents an independent infection with either cSki or MIGR1 Comparison of GFP+ve LKS+ infected with MIGR1 and cSki
Project description:To define target genes of the intestine-restricted transcription factor (TF) CDX2 in intestinal stem cells, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq). We used RNA-sequencing to profile gene expression changes during cell differentiation from mouse intestinal stem cells to mature villus cells, as well as genes perturbed in intestinal stem cells upon loss of Cdx2. We find thousands of genes that change in expression during cell differentiation, including known stem cell and mature markers. Upon loss of Cdx2, hundreds of genes are up and down-regulated in intestinal stem cells, some of which are also bound by CDX2 nearby and constitute candidate direct target genes. CDX2 ChIP-Seq analysis of isolated mouse intestinal stem cells. RNA seq analysis of control mouse villus cells, control intestinal stem cells and Cdx2-deleted intestinal stem cells.
Project description:We perfomed ChIP-seq using KDM5A antibodies in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We show that the cistrome of the H3K4 demethylase KDM5A is affected by AKT inhibition. Comparison of genome-wide KDM5A binding after AKT inhibition vs vehicle
Project description:We perfomed ChIP-seq using H3K4me3 antibodies in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We demonstrate that at a selected group of loci H3K4me3 is affected by AKT inhibition. Comparison of genome-wide H3K4me3 binding after AKT inhibition vs vehicle
Project description:We identified genome-wide PRR9 targets by conducting chromatin immunoprecipitation followed by high-throughput sequencing. Plants were grown in cycling 12 h light/12 h dark for two weeks before harvesting at ZT4. The four samples include the immunoprecipitated and input control for prr9-1 PRR9::HA-PRR9 CCR2::LUC #109 (HA9) and the prr9-1 (s9c) parental control. PRR5 PRR7 and TOC1 raw data available from the following Series: PRR5: GSE36361 TOC1: GSE35952 PRR7: GSE49282 (GSM1196649 and GSM1196650)
Project description:Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells. Examination of histone H3K27Ac modifications in various breast cancer cell lines.