Trimethylation of Histone H3 Lysine 4 is an Epigenetic Mark at Regions Escaping Mammalian X Inactivation

It is now estimated that 150-200 genes clustered in several discrete regions escape X inactivation in somatic cells of human females by unknown mechanisms. Here, we show that although the human female inactive X chromosome is largely devoid of histone 3 lysine 4 trimethylation (H3K4me3), regions that are known to escape X inactivation, including the pseudoautosomal regions, are enriched with this modification. Also, H3K4me3, unlike H3K4me2 and H4 and H3 acetylation, is restricted to discrete regions on metaphase chromosomes. In contrast to humans, there are only a few genes that are known to escape X inactivation in the mouse. Therefore, we examined mouse female somatic cells with H3K4me3 to identify candidate regions with genes that escape X inactivation. We found the mouse female inactive X in somatic cells and the male inactive X in meiosis to have seven discrete regions that are enriched with H3K4me3. Furthermore, RNA polymerase II is largely excluded from the XY body at male pachytene except for several discrete regions on the X and Y suggesting the presence of regions that also escape sex chromosome inactivation during male meiosis.     

Loss of H3 K79 Trimethylation Leads to Suppression of Rtt107-dependent DNA Damage Sensitivity through the Translesion Synthesis Pathway

Genomic integrity is maintained by the coordinated interaction of many DNA damage response pathways, including checkpoints, DNA repair processes, and cell cycle restart. In Saccharomyces cerevisiae, the BRCA1 C-terminal domain-containing protein Rtt107/Esc4 is required for restart of DNA replication after successful repair of DNA damage and for cellular resistance to DNA-damaging agents. Rtt107 and its interaction partner Slx4 are phosphorylated during the initial phase of DNA damage response by the checkpoint kinases Mec1 and Tel1. Because the natural chromatin template plays an important role during the DNA damage response, we tested whether chromatin modifications affected the requirement for Rtt107 and Slx4 during DNA damage repair. Here, we report that the sensitivity to DNA-damaging agents of rtt107Δ and slx4Δ mutants was rescued by inactivation of the chromatin regulatory pathway leading to H3 K79 trimethylation. Further analysis revealed that lack of Dot1, the H3 K79 methyltransferase, led to activation of the translesion synthesis pathway, thereby allowing the survival in the presence of DNA damage. The DNA damage-induced phosphorylation of Rtt107 and Slx4, which was mutually dependent, was not restored in the absence of Dot1. The antagonistic relationship between Rtt107 and Dot1 was specific for DNA damage-induced phenotypes, whereas the genomic instability caused by loss of Rtt107 was not rescued. These data revealed a multifaceted functional relationship between Rtt107 and Dot1 in the DNA damage response and maintenance of genome integrity.     

小鼠孤雌胚与体内正常胚H3K27三甲基化模式的差异

为了考察小鼠(Mus musculus)孤雌激活胚胎H3K27三甲基化模式与体内正常胚胎之间的差异,以及曲古抑菌素A(TSA)对孤雌胚H3K27三甲基化水平的影响,探究表观遗传修饰对孤雌胚胎发育的作用。首先,用H3K27me3特异性抗体对MⅡ期卵母细胞染色,利用激光共聚焦对其荧光强度进行检测,结果发现该时期的甲基化荧光强度相对较低。接着,采用同样的方法对小鼠孤雌胚胎和体内正常胚胎植入前各时期的H3K27me3模式进行比较,结果显示,从2-细胞到囊胚期孤雌组呈现逐渐升高的趋势,与体内组变化趋势完全相反,且总体平均荧光强度较体内组普遍偏低。孤雌胚胎经TSA处理后,处理组和未处理组在前三个时期虽然没有显著性差异(P0.05),但是处理之后的H3K27三甲基化水平有所提高,囊胚期与未处理组相比有显著性差异(P0.05)。以上结果表明,小鼠孤雌胚胎的H3K27三甲基化模式与体内胚胎之间存在着巨大的差异,这可能是造成孤雌胚胎发育能力差的重要原因之一。TSA处理对H3K27me3模式造成了一定的影响,使体外培养环境有所改善,这可能对提高孤雌胚胎发育能力具有一定的意义。     

Methylation of H3 K4 and K79 is not strictly dependent on H2B K123 ubiquitylation

Covalent modifications of histone proteins have profound consequences on chromatin structure and function. Specific modification patterns constitute a code read by effector proteins. Studies from yeast found that H3 trimethylation at K4 and K79 is dependent on ubiquitylation of H2B K123, which is termed a “trans-tail pathway.” In this study, we show that a strain unable to be ubiquitylated on H2B (K123R) is still proficient for H3 trimethylation at both K4 and K79, indicating that H3 methylation status is not solely dependent on H2B ubiquitylation. However, additional mutations in H2B result in loss of H3 methylation when combined with htb1-K123R. Consistent with this, we find that the original strain used to identify the trans-tail pathway has a genomic mutation that, when combined with H2B K123R, results in defective H3 methylation. Finally, we show that strains lacking the ubiquitin ligase Bre1 are defective for H3 methylation, suggesting that there is an additional Bre1 substrate that in combination with H2B K123 facilitates H3 methylation.     

Changes in H3K79 methylation during preimplantation development in mice

The gene expression pattern of differentiated oocytes is reprogrammed into that of totipotent preimplantation embryos before and/or after fertilization. To elucidate the mechanisms of genome reprogramming, we investigated histone H3 lysine 79 dimethylation (H3K79me2) and trimethylation (H3K79me3) in oocytes and preimplantation embryos via immunocytochemistry. In somatic cells and oocytes, H3K79me2 was observed throughout the genome, whereas H3K79me3 was localized in the pericentromeric heterochromatin regions in which there are no active genes. Because H3K79me2 is considered an active gene marker, H3K79 methylation seems to have differing functions depending on the number of methyl groups added on the same residues. Both H3K79me2 and H3K79me3 decreased soon after fertilization, and the hypomethylated state was maintained at interphase (before the blastocyst stage), except for a transient increase in H3K79me2 at mitosis (M phase). H3K79me3 was not detected throughout preimplantation, even at M phase. To investigate the involvement of H3K79me2 in genome reprogramming, somatic nuclei were transplanted into enucleated oocytes. H3K79me2 in these nuclei was demethylated following parthenogenetic activation. However, the nuclei that had been transplanted into the parthenogenetic embryos 7 h after activation were not demethylated. This suggests that the elimination of H3K79 methylation after fertilization is involved in genomic reprogramming.     

Recognition of Histone H3K4 Trimethylation by the Plant Homeodomain of PHF2 Modulates Histone Demethylation

Distinct lysine methylation marks on histones create dynamic signatures deciphered by the “effector” modules, although the underlying mechanisms remain unclear. We identified the plant homeodomain- and Jumonji C domain-containing protein PHF2 as a novel histone H3K9 demethylase. We show in biochemical and crystallographic analyses that PHF2 recognizes histone H3K4 trimethylation through its plant homeodomain finger and that this interaction is essential for PHF2 occupancy and H3K9 demethylation at rDNA promoters. Our study provides molecular insights into the mechanism by which distinct effector domains within a protein cooperatively modulate the “cross-talk” of histone modifications.     

Trimethylation of histone H3K4 is associated with the induction of fructose-inducible genes in rat jejunum

We previously reported that fructose force-feeding rapidly induces jejunal Slc2a5 gene expression in rats. In this study, we conducted microarray analyses using total RNA to identify genes upregulated in rat jejunum by fructose force-feeding. Rats were force-fed fructose, glucose or distilled water for 6h. Genes such as Slc2a5, Cdkn1c, Cabp2, Ranbp3, Vwce and Gcgr were induced by force-feeding with fructose compared with glucose or distilled water. Chromatin immunoprecipitation assays revealed that trimethylation of histone H3K4, and acetylation of histones H3 and H4, on the transcribed region of these fructose-inducible genes were enhanced by force-feeding of fructose, but not glucose or distilled water. These results suggest that the induction of genes in the rat jejunum by fructose force-feeding is coordinately regulated by histone modifications, particularly trimethylation of histone H3K4.     

Histone H3K79 methylation by DOT1L promotes Aurora B localization at centromeres in mitosis

1. Download : Download high-res image (192KB)
2. Download : Download full-size image

     

Kinetics of Re-establishing H3K79 Methylation Marks in Global Human Chromatin

We employ a stable isotope strategy wherein both histones and their methylations are labeled in synchronized human cells. This allows us to differentiate between old and new methylations on pre-existing versus newly synthesized histones. The strategy is implemented on K79 methylation in an isoform-specific manner for histones H3.1, H3.2, and H3.3. Although levels of H3.3K79 monomethylation are higher than that of H3.2/H3.1, the rate of establishing the K79 methylation is the same for all three isoforms. Surprisingly, we find that pre-existing “old” histones continue to be K79-monomethylated and -dimethylated at a rate equal to the newly synthesized histones. These observations imply that some degree of positional “scrambling” of K79 methylation occurs through the cell cycle.     

Trimethylation of histone H3K76 by Dot1B enhances cell cycle progression after mitosis in Trypanosoma cruzi

Dot1 enzymes are histone methyltransferases that mono-, di- and trimethylate lysine 79 of histone H3 to affect several nuclear processes. The functions of these different methylation states are still largely unknown. Trypanosomes, which are flagellated protozoa that cause several parasitic diseases, have two Dot1 homologues. Dot1A catalyzes the mono- and dimethylation of lysine 76 during late G2 and mitosis, and Dot1B catalyzes trimethylation, which is a modification found in all stages of the cell cycle. Here, we generated Trypanosoma cruzi lines lacking Dot1B. Deletion of one allele resulted in parasites with increased levels of mono- and dimethylation and a reduction in H3K76me3. In the full knockout (DKO), no trimethylation was observed. Both the DKO and the single knockout (SKO) showed aberrant morphology and decreased growth due to cell cycle arrest after G2. This phenotype could be rescued by caffeine in the DKO, as caffeine is a checkpoint inhibitor of the cell cycle. The knockouts also phosphorylated γH2A without producing extensive DNA breaks, and Dot1B-depleted cells were more susceptible to general checkpoint kinase inhibitors, suggesting that a lack of H3K76 trimethylation prevents the initiation and/or completion of cytokinesis.     

组蛋白 H3K79同型半胱氨酸修饰位点在神经管畸形中的作用

目的:探讨人类胚胎脑组织中是否存在H3K79同型半胱氨酸修饰(H3K79Hcy)及其在神经管畸形(NTDs)中的作用。方法:通过质谱检测组蛋白H3K79是否存在同型半胱氨酸修饰位点。进一步合成包含组蛋白H3K79位点的同型半胱氨酸(Hcy)修饰的肽段,并与牛血清白蛋白(BSA)偶联后免疫兔子得到抗组蛋白H3K79Hcy多克隆抗体,并对抗体进行特异性检测;采用此抗H3K79Hcy抗体比较人类高Hcy NTDs样本和正常对照样本的H3K79Hcy水平。结果:(1)人胚胎组织组蛋白H3K79位点存在同型半胱氨酸修饰;(2)高Hcy水平NTDs脑组织中H3K79Hcy修饰水平高于正常对照(P0.05)。结论:人胚胎组织存在H3K79Hcy修饰,此修饰异常可能促进神经管畸形的发生。