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Epigenetic marks are important factors regulating the pluripotency and differentiation of human embryonic stem cells (hESCs). In this study, we analyzed H3K9 acetylation, an epigenetic mark associated with transcriptionally active chromatin, during endoderm-like differentiation of hESCs. ChIP-on-chip analysis revealed that differentiation results in a genome-wide decrease in promoter H3K9 acetylation. Among the 24,659 promoters analyzed, only 117 are likely to be involved in pluripotency, while 25 acetylated promoters are likely to be responsible for endoderm-like differentiation. In pluripotent hESCs, the chromosomes with the highest absolute levels of H3K9 acetylation are chromosomes 1, 6, 2, 17, 11, and 12 (listed in order of decreasing acetylation). Chromosomes 17, 19, 11, 20, 22, and 12 are the most prone to differentiation-related changes (both increased acetylation and deacetylation). When chromosome size (in Mb) was accounted for, the highest H3K9 acetylation levels were found on chromosome 19, 17, 6, 12, 11, and 1, and the greatest differentiation-associated decreases in H3K9 acetylation occurred on chromosomes 19, 17, 11, 12, 16, and 1. The gene density and size of individual chromosomes were strongly correlated with the levels of H3K9 acetylation. Our analyses point to chromosomes 11, 12, 17, and 19 as being critical for hESC pluripotency and endoderm-like differentiation. J. Cell. Physiol. 219: 677–687, 2009. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

It has become evident that epitranscriptome events, mediated by specific enzymes, regulate gene expression and, subsequently, cell differentiation processes. We show that methyltransferase-like proteins METTL3/METTL14 and N6-adenosine methylation (m6A) in RNAs are homogeneously distributed in embryonic hearts, and histone deacetylase (HDAC) inhibitors valproic acid and Trichostatin A (TSA) up-regulate METTL3/METTL14 proteins. The levels of METTL3 in mouse adult hearts, isolated from male and female animals, were lower in the aorta and pulmonary trunks when compared with atria, but METT14 was up-regulated in the aorta and pulmonary trunk, in comparison with ventriculi. Aging caused METTL3 down-regulation in aorta and atria in male animals. Western blot analysis in differentiated mouse embryonic stem cells (mESCs), containing 10–30 percent of cardiomyocytes, showed METTL3/METTL14 down-regulation, while the differentiation-induced increased level of METTL16 was observed in both wild type (wt) and HDAC1 depleted (dn) cells. In parallel, experimental differentiation in especially HDAC1 wild type cells was accompanied by depletion of m6A in RNA. Immunofluorescence analysis of individual cells revealed the highest density of METTL3/METTL14 in α-actinin positive cardiomyocytes when compared with the other cells in the culture undergoing differentiation. In both wt and HDAC1 dn cells, the amount of METTL16 was also up-regulated in cardiomyocytes when compared to co-cultivated cells. Together, we showed that distinct anatomical regions of the mouse adult hearts are characterized by different levels of METTL3 and METTL14 proteins, which are changed during aging. Experimental cell differentiation was also accompanied by changes in METTL-like proteins and m6A in RNA; in particular, levels and distribution patterns of METTL3/METTL14 proteins were different from the same parameters studied in the case of the METTL16 protein. [ABSTRACT FROM AUTHOR]

Cell differentiation into cardiomyocytes requires activation of differentiation-specific genes and epigenetic factors that contribute to these physiological processes. This study is focused on the in vitro differentiation of mouse embryonic stem cells (mESCs) induced into cardiomyocytes. The effects of clinically promising inhibitors of histone deacetylases (HDACi) on mESC cardiomyogenesis and on explanted embryonic hearts were also analyzed. HDAC1 depletion caused early beating of cardiomyocytes compared with those of the wild-type (wt) counterpart. Moreover, the adherence of embryonic bodies (EBs) was reduced in HDAC1 double knockout (dn) mESCs. The most important finding was differentiation-specific H4 deacetylation observed during cardiomyocyte differentiation of wt mESCs, while H4 deacetylation was weakened in HDAC1-depleted cells induced to the cardiac pathway. Analysis of the effect of HDACi showed that Trichostatin A (TSA) is a strong hyperacetylating agent, especially in wt mESCs, but only SAHA reduced the size of the beating areas in EBs that originated from HDAC1 dn mESCs. Additionally, explanted embryonic hearts (e15) responded to treatment with HDACi: all of the tested HDACi (TSA, SAHA, VPA) increased the levels of H3K9ac, H4ac, H4K20ac, and pan-acetylated lysines in embryonic hearts. This observation shows that explanted tissue can be maintained in a hyperacetylation state several hours after excision, which appears to be useful information from the view of transplantation strategy and the maintenance of gene upregulation via acetylation in tissue intended for transplantation. [ABSTRACT FROM AUTHOR]

Abstract Histone posttranslational modifications regulate diverse nuclear functions, including DNA repair. Here, we use mass spectrometry, western blotting, immunohistochemistry and advanced confocal microscopy in order to show radiation-specific changes in the histone signature. We studied wild-type mouse embryonic stem cells (mESCs) and mESCs with a depletion of histone deacetylase 1 (HDAC1), which plays a role in DNA repair. Irradiation by γ-rays increased the S139 phosphorylation of histone H2AX but reduced the level of the H3K9-R17 peptide, which contains S10 phosphorylation (H3S10ph). On an individual cellular level, H3S10ph was low in highly γH2AX-positive UV laser-induced DNA lesions, and this nuclear distribution pattern was not changed by HDAC1 depletion. Despite this fact, spontaneous γH2AX-positive DNA lesions colocalized with large H3S10ph-positive nuclear bodies that appear in the G2 phase of the cell cycle. Similarly, by FLIM-FRET analysis, we observed an interaction between H3S10ph and γH2AX in the G2 phase. However, this interaction was reduced when cells were exposed to γ-rays. A mutual link between H3S10ph and γH2AX was not observed in the G1 phase of the cell cycle. Together, our data show that despite the fact that H3S10ph is not directly involved in DNA repair, a decrease in H3S10 phosphorylation and weakened interaction between H3S10ph and γH2AX is a result of radiation-induced damage of the genome. In this case, γ-irradiation also decreased the number of cells in the G1 phase, characterized by no interaction between H3S10ph and γH2AX. Graphical abstract (A) Irradiation by γ-rays (red line) reduced H3S10ph levels. However, (B) H3S10ph was intact in the γH2AX-positive microirradiated genomic region. (C) Despite the fact that H3S10ph- and γH2AX-positive foci colocalized (interacted) in the G2 phase of the cell cycle, radiation-induced H3S10ph dephosphorylation was not directly linked to DNA repair processes, but instead (D) H3S10ph dephosphorylation was caused by a radiation-induced cell number decrease in the G1 phase. G1 phase was characterized by no interaction between H3S10ph and γH2AX (mentioned in panel C). Together, H3S10ph contributes to the function of γH2AX in DNA repair taking place in G2 phase. Image 1 Highlights • Irradiation by γ-rays increased γH2AX but reduced the level of H3S10ph. • A mutual link between H3S10ph and γH2AX was not observed in the G1 phase of the cell cycle. • An interaction between γH2AX and H3S10ph was found in the G2 phase. • H3S10ph contributes to the function of γH2AX in homologous recombination repair. [ABSTRACT FROM AUTHOR]