Project description:Microarray transcriptome analysis of siMock and siACL HCT116 cells treated with 0, 0.5, 2.0, and 5.0 mM butyrate over three days. Gene expression is measured at control cells (siMock) and ACL-depleted (siACL) cells with 4 dosages (0, 0.5, 2.0, and 5.0 mM) of butyrate treatments
Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.
Project description:EHF and CDX1 co-operate to drive differentation of CRC cells. To identify the change in chromatin remodelling induced by these transcription factors, EHF and CDX1 were stably re-expressed in poorly differentiated HCT116 CRC cells and ATAC-seq analysis performed.
Project description:To investigate the molecular mechanism how butyrate promoter differentiation of naïve T cells into regulatory T cells Examination of acetylated histone H3 during the differentiation of regulatory T cells in the presence or absence of butyrate
Project description:Expression in organoids dervied from the ileum of WT C57Bl/6 mice stimulated with butyrate, IL-13, or butyrate + IL-13. Intestinal organoids were stimulated with butyrate for 48hrs, then IL-13 for 72 hrs. RNA was isolated using RNeasy Kit (Qiagen). Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.
Project description:Butyrate, a gut microbial metabolite, has beneficial effects on glucose homeostasis and has become an attractive drug target for type 2 diabetes (T2D). Recently, we showed that butyrate protects pancreatic beta cells against cytokine-induced dysfunction. In this study, we explored the underlying mechanisms of butyrate action. Pancreatic islets were exposed to a non-cytotoxic concentration of interleukin 1β (IL-1β) for ten days to mimic the low-grade inflammation in T2D. An isoform-selective histone deacetylase 3 (HDAC3) inhibitor normalized IL-1β-reduced GSIS and insulin content similar to the effect of butyrate. In contrast, FFAR2/3 agonists failed to normalize IL-1β-induced impairment of GSIS and reduced insulin content. Butyrate, irrespective of IL-1β, inhibited HDAC activity and increased histone H3 and H4 acetylation by 3- and 10-fold, respectively. Genome-wide analysis of histone H3K27 acetylation (H3K27ac) revealed that butyrate mainly increased H3K27ac at promoter regions (~68 %), while H3K27ac peaks regulated by IL-1β were more equally distributed at promoters (~33 %), introns (~23 %) and intergenic regions (~23 %). Gene ontology analysis showed that butyrate increased IL-1β-reduced H3K27ac levels near several genes related to hormone secretion and reduced IL-1β-increased H3K27ac levels near genes associated with inflammatory responses . Butyrate alone increased H3K27ac near many genes related to MAPK signaling, hormone secretion and differentiation, and decreased H3K27ac at genes involved in cell replication. Together, these results suggest that butyrate prevents IL-1β-induced beta cell dysfunction by inhibition of HDACs resulting in changes in H3K27ac levels at genes relevant for beta cell function and inflammatory responses.
Project description:In the mammalian intestine, crypts of Leiberkühn house intestinal epithelial stem /progenitor cells at their base. We found that the presence of this structure was supported by the physiologic role of a prominent bacterial metabolite, butyrate. This bacterially-produced short chain fatty acid inhibited intestinal epithelial proliferation at physiologic concentrations. During homeostasis, butyrate did not suppress epithelial stem proliferation because it was metabolized by differentiated colonocytes. Provision of butyrate access to stem/progenitor cells either through mucosal injury or application to a crypt-less host led to inhibition of proliferation. The mechanism was dependent on HDAC inhibition in stem cells and the transcription factor Foxo3. Thus, the mammalian crypt unit structure provides energy for differentiated cells at a distance from the crypt base and this action prevents suppression of stem/progenitor proliferation. In total 4 samples were analyzed from 2 independent experiments. Two samples of colonic stem cells treated with 1mM Butyrate and two samples of colonic stem cells treated with 1mM NaCl (mock) as a control