Project description:ChIP-Seq analysis revealed that suberoylanilidehydroxamic acid (SAHA) increases genome-wide H4 acetylation in differentially regulated genes, except for the 500 bp upstream of transcription start sites (TSS). Chromatin immunoprecipitation (ChIP) with massively parallel high throughput sequencing (Seq) was used to map genome-wide histone H4 acetylation (K4/7/11/15) in the presence or absence of SAHA in differentiating MC3T3 sc4 osteoblasts.
Project description:Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.
Project description:To address a target gene spectrum of CpBV-H4, we need to analyze total gene expression in response to a specific expression of CpBV-H4 by a transient expression technique.
Project description:The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2∆ cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. Furthermore, the influence of Sas2 on gene expression was investigated in RNA expression arrays.
Project description:To explore the genome-wide gene expression changes induced by the K31R mutation in the histone H4 protein, we performed RNA-sequencing analysis in U2OS cells expressing either wildtype H4 or K31R mutant H4. We found that the lysine (K) to arginine (R) mutation mainly affected oxidative phosphorylation, mtiochondria dysfunction and et al, but not DNA damage signaling pathways.
Project description:Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where histone variant H4.V is deposited. A previously generated cell line (Siegel et al., 2009) in which both endogenous H4.V alleles are knockout out and ectopic overexpression of a Ty1-tagged version of H4.V can be induced was used. During the ChIP experiment, the DNA was digested with MNase to obtain mononucleosomes. Nucleosomes containing H4.V were pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and mononucleosomal DNA is purified and prepared for Illumina sequencing.