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SUMMARY Differences in global levels of histone acetylation occur in normal and cancer cells, although the reason why cells regulate these levels has been unclear. Here we demonstrate a role for histone acetylation in regulating intracellular pH (pHi). As pHi decreases, histones are globally deacetylated by histone deacetylases (HDACs), and the released acetate anions are coexported with protons out of the cell by monocarboxylate transporters (MCTs), preventing further reductions in pHi. Conversely, global histone acetylation increases as pHi rises, such as when resting cells are induced to proliferate. Inhibition of HDACs or MCTs decreases acetate export and lowers pHi, particularly compromising pHi maintenance in acidic environments. Global deacetylation at low pH is reflected at a genomic level by decreased abundance and extensive redistribution of acetylation throughout the genome. Thus, acetylation of chromatin functions as a rheostat to regulate pHi with important implications for mechanism of action and therapeutic use of HDAC inhibitors.

Adenovirus e1a induces quiescent human cells to replicate. We found that e1a causes global relocalization of the RB (retinoblastoma) proteins (RB, p130, and p107) and p300/CBP histone acetyltransferases on promoters, the effect of which is to restrict the acetylation of histone 3 lysine-18 (H3K18ac) to a limited set of genes, thereby stimulating cell cycling and inhibiting antiviral responses and cellular differentiation. Soon after expression, e1a binds transiently to promoters of cell cycle and growth genes, causing enrichment of p300/CBP, PCAF (p300/CBP-associated factor), and H3K18ac; depletion of RB proteins; and transcriptional activation. e1a also associates transiently with promoters of antiviral genes, causing enrichment for RB, p130, and H4K16ac; increased nucleosome density; and transcriptional repression. At later times, e1a and p107 bind mainly to promoters of development and differentiation genes, repressing transcription. The temporal order of e1a binding requires its interactions with p300/CBP and RB proteins. Our data uncover a defined epigenetic reprogramming leading to cellular transformation.The adenovirus small e1a oncoprotein interacts with multiple cellular factors to induce cell cycling in G 0 -arrested cells to favor viral replication. Mutations of e1a regions that interact with the RB proteins or p300/CBP [cyclic adenosine monophosphate response element-binding protein (CREB)-binding protein] result in loss of e1a-transforming and mitogenic activities (1-3) (figs. S1 and S2). Binding of e1a to p300/CBP inhibits transcriptional activation by certain enhancers (4); however, it is unclear how this interaction promotes cell cycling and why it is required for e1a oncogenicity. The e1a-p300/CBP interaction causes a factor of ~3 reduction in total cellular histone 3 Lys 18 acetylation (H3K18ac) specifically (5). Therefore, we sought to determine how e1a affects the genome-wide distributions of its interacting cellular factors as well as histone modifications (including H3K18ac) to establish an oncogenic gene expression program. Using chromatin immunoprecipitation (ChIP) combined with microarrays (6), we examined the genome-wide binding of e1a at 2, 6, 12, and 24 hours (here and below, all times are postinfection) of confluent, contact-inhibited human IMR90 primary fibroblasts (ATCC CCL-186) in which e1a induces entry into S phase between 18 and 24 hours ( fig. S2). We used an Agilent microarray containing probes for ~17,000 promoters, tiling an 8-kb region, which we divided computationally into 16 fragments of 500 base pairs (bp) each, spanning -5.5 to +2.5 kb of the transcription start site (TSS). Cells were infected with Ad5 mutant dl1500, which expresses only the small e1a protein (7). Using unbiased partitional clustering, we grouped the genes primarily into three clusters that captured the main trends in the data. We calculated a Z score to indicate the degree of enrichment for a given factor in each cluster.During the 24-hour period after expression, at a cutoff of Z ≥ 2, e1a bou...

Summary Endothelium in embryonic hematopoietic tissues generates hematopoietic stem/progenitor cells; however, it is unknown how its unique potential is specified. We show that transcription factor Scl/Tal1 is essential for both establishing the hematopoietic transcriptional program in hemogenic endothelium and preventing its misspecification to a cardiomyogenic fate. Scl−/− embryos activated a cardiac transcriptional program in yolk sac endothelium, leading to the emergence of CD31+Pdgfrα+ cardiogenic precursors that generated spontaneously beating cardiomyocytes. Ectopic cardiogenesis was also observed in Scl−/− hearts, where the disorganized endocardium precociously differentiated into cardiomyocytes. Induction of mosaic deletion of Scl in Sclfl/fl Rosa26Cre-ERT2 embryos revealed a cell-intrinsic, temporal requirement for Scl to prevent cardiomyogenesis from endothelium. Scl−/− endothelium also upregulated the expression of Wnt antagonists, which promoted rapid cardiomyocyte differentiation of ectopic cardiogenic cells. These results reveal unexpected plasticity in embryonic endothelium such that loss of a single master regulator can induce ectopic cardiomyogenesis from endothelial cells.

Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here, we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 shows an increase of relative 5meC levels at the transcription start site and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo.DOI: http://dx.doi.org/10.7554/eLife.06205.001