Project description:Epigenetic changes in DNA and chromatin are implicated in organogenesis and cell differentiation. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach (ChIP-seq) we analyses the enrichment of H3K79me2 and H3K4me3 (histone methylation marks associated with transcriptional activation) and H3K27me3 and H3K9me3 (histone methylation marks associated with transcriptional repression) in neonatal and adult cardiomyocytes. The histone methylation profile obtained was correlated with an Illumina gene expression profile from the same samples. Our results demonstrate that histone methylation, and in particular the DOT1L-mediated H3K79me2 mark, drives cardiomyogenesis through the definition of a specific transcriptional landscape Profiling of H3K79me2, H3K4me3, H3K27me3 and H3K9me3 in neonatal and adult cardiomyocytes
Project description:Epigenetic changes in DNA and chromatin are implicated in organogenesis and cell differentiation. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach (ChIP-seq) we analyses the enrichment of H3K79me2 and H3K4me3 (histone methylation marks associated with transcriptional activation) and H3K27me3 and H3K9me3 (histone methylation marks associated with transcriptional repression) in neonatal and adult cardiomyocytes. The histone methylation profile obtained was correlated with an Illumina gene expression profile from the same samples. Our results demonstrate that histone methylation, and in particular the DOT1L-mediated H3K79me2 mark, drives cardiomyogenesis through the definition of a specific transcriptional landscape
Project description:Genome-wide gene expression analysis at different stages of cardiomyocyte differentiation (undifferentiated mouse embryonic stem cells, neonatal mouse cardiomyocytes and adult mouse cardiomyocytes). Results provide important information on the differential expressed genes between undifferentiated mouse embrionic stem cells (mES) and mouse cardiomyocytes (CM) and also between cardiomyocytes from neonatal (CMp) and adult stages (CMa). This dataset allowed us to compare the expression profile of mES, CMp and CMa with the epigenetic profile of histone methylation generated with ChIP-seq experiments. Total RNA was obtained from biological triplicate of undifferentiated mouse embryonic stem cells (mES), neonatal mouse cardiomyocytes (CMp) and adult mouse cardiomyocytes (CMa)
Project description:Genome-wide gene expression analysis at different stages of cardiomyocyte differentiation (undifferentiated mouse embryonic stem cells, neonatal mouse cardiomyocytes and adult mouse cardiomyocytes). Results provide important information on the differential expressed genes between undifferentiated mouse embrionic stem cells (mES) and mouse cardiomyocytes (CM) and also between cardiomyocytes from neonatal (CMp) and adult stages (CMa). This dataset allowed us to compare the expression profile of mES, CMp and CMa with the epigenetic profile of histone methylation generated with ChIP-seq experiments.
Project description:Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Histone H3 or H4 tri-methylation ChIP-Seq in singlicate from murine embryonic stem (ES) cells, ES-derived neural precursor cells, and embryonic fibroblasts.
Project description:DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis. The cross-talk between DNA methylation and Polycomb-dependent H3K27me3 histone mark has been reported in a number of organisms and both marks are known to be required for proper developmental progression. Here we provide genome-wide DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) maps for three stages (dome, 24hpf and 48hpf) of zebrafish (Danio rerio) embryogenesis, as well as all analytical and methodological details associated with the generation of this dataset. DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) profling of zebrafish embryogenesis
Project description:Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the understanding of fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing from several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans. Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining active or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes. This study is the first genome-wide characterization of the histone code from a Stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
2015-05-08 | PXD002148 | Pride
Project description:Neonatal and adult cardiomyocytes
Project description:Epigenetic states defined by chromatin can be maintained through mitotic cell division. However, it remains unknown how histone-based information is transmitted. Here we combine nascent chromatin capture (NCC) and triple-SILAC labelling to track histone modifications and histone variants during DNA replication and across the cell cycle. We show that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA. Di- and tri-methylation marks are diluted two-fold upon DNA replication, as a consequence of new histone deposition. Importantly, within one cell cycle all PTMs are restored. In general, new histones are modified to mirror the parental histones. However, H3K9me3 and H3K27me3 are propagated by continuous modification of parental and new histones, because the establishment of these marks extends over several cell generations. Together, our results reveal how histone marks propagate and demonstrate that chromatin states oscillate within the cell cycle.
Project description:In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation. Whole genome methylation maps of idm3-3, mbd7-2(CS876032) and Col-0 WT were generated using BS-seq