Project description:Genome-wide maps of nucleosome positioning in mouse ES cells with control shRNA and on Smarcad1 KD. MNase-seq data for human colo829 cells are also included.
Project description:Genome-wide maps of SMARCAD1 binding and histone modification H3R26Cit in mouse ES cells, histone modification H3K9me3, H3K4me3, H3K27Ac in Smarcad1 KD mouse ES cells, and histone modification H3K9me3 in mouse ES cells after PADI inhibition. Together with RNA-seq data for mouse ICM, blastocyst, embryonic stem cells and Smarcad1 KD cells.
Project description:Examination of the repositioning of nucleosome and hexasome-sized particles induced by the SMARCAD1 family proteins in cells support the hexasome-binding mode. Our findings reveal a new mode of chromatin regulation, wherein the nucleosome intermediates are specially remodeled through an ATP-dependent process.
Project description:Nucleosome positioning is critical to chromatin accessibility, and is associated with gene expression programs in cells. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array surrounding the transcription start sites (TSSs ) of active genes and DNase I hypersensitive sites (DHSs). However, cells exhibit remarkable expression heterogeneity in response to active signaling even in a homogenous population of cells, which may be related to the heterogeneity in chromatin accessibility. Here, we report a technique, termed single-cell MNase-seq (scMNase-seq), to measure genome-wide nucleosome positioning and chromatin accessibility simultaneously in single cells. Application of scMNase-seq to NIH3T3, mouse primary naïve CD4 T and embryonic stem cells (mESC) reveals two novel principles of nucleosome organization: (1) nucleosomes surrounding TSSs of silent genes or in heterochromatin regions show large positioning variation across different cells but are highly uniformly spaced along the nucleosome array and, (2) In contrast, nucleosomes surrounding TSSs of active genes and DHSs show small positioning variation across different cells but show relatively low spacing uniformness along the nucleosome array. We found a bimodal distribution of nucleosome spacing at DHSs, which corresponds to inaccessible and accessible states and is associated with nucleosome variation and accessibility variation across cells. Nucleosome variation within single cells is smaller than that across cells and variation within the same cell type is smaller than that across cell types. A large fraction of naïve CD4 T cells and mESCs show depleted nucleosome occupancy at the de novo enhancers detected in their respectively differentiated lineages, revealing the existence of cells primed for differentiation to specific lineages in undifferentiated cell populations.
Project description:We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.
Project description:We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a pronounced Nucleosome Depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. This global similarity, however, does not reflect a static evolutionary pattern, as nucleosome positioning at specific genes diverged rapidly leaving practically no similarity between S. cerevisiae and C. glabrata orthologs (~50 Myr). We show that this rapid divergence in nucleosome positioning contrasts a conserved pattern of gene expression, consistent with the idea that divergence of nucleosome patterns has a limited effect on gene expression as many different configurations can support the same regulatory outcome.
Project description:Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert embryonic stem cells (ESCs) to 2C-like cells. This conversion is marked by a global reorganization and dispersion of H3K9me3-heterochromatin foci, which are then reversibly formed upon re-entry into pluripotency. Profiling the chromatin-bound proteome (chromatome) by genome capture of ESCs transitioning to 2C-like cells, we uncover chromatin regulators involved in de novo heterochromatin formation. We identified TOPBP1 and investigated its binding partner SMARCAD1. SMARCAD1 and TOPBP1 associate with H3K9me3-heterochromatin in ESCs. Interestingly, the nuclear localization of SMARCAD1 is lost in 2C-like cells. SMARCAD1 or TOPBP1 depletion in mouse embryos lead to developmental arrest, reduction of H3K9me3 and remodeling of heterochromatin foci. Collectively, our findings contribute to comprehending the maintenance of chromocenters during early development.
Project description:This SuperSeries is composed of the following subset Series: GSE40910: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] GSE40948: Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq] GSE40951: Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] Refer to individual Series