Regulation Of H3K4 Methylation Research Articles

Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation.

From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.

190 SPINDLIN 1 IS REQUIRED FOR METAPHASE II ARREST IN PORCINE OOCYTES

Spindlin 1 (Spin1), is a histone methylation effecter protein. It can specifically recognise and bind to trimethylated histone 3 lysine 4 (H3K4). Spin1 localizes to the active rDNA repeats and facilitates the expressions of rRNA genes. For exploring the function of Spin1 in porcine oocyte and embryo development, siRNA of Spin1 (siSpin1) was used in the present study. Messenger RNA level of Spin1 was more highly expressed in the ovary than other tissues. During oocyte maturation, Spin1 was highly expressed from germinal vesicle to metaphase II stage in oocyes but sharply decreased after zygotic genome activation. The SPIN1 protein was localised to the cytoplasm and showed a similar expression pattern with mRNA through all stages of early embryonic development. Spin1 was successfully knocked down by siRNA injection. The siRNA of green fluorescent protein (siGFP) was used as positive control, and distilled water (DW) was used as a negative control. All were injected at metaphase II stage. Oocyte maturation was not altered by siSpin1 microinjection, but the rate of embryo development was significantly decreased from 4-cell stage when compared with the control group. The Spin1 had an effect on the blastocyst formation, which may have been altered by polymerase I-mediated rRNA gene transcription via regulation of H3K4 methylation. On the other hand, pronuclear formation was reduced by Spin1 siRNA. All data were analysed with a one-way analysis of variance, and differences between treatment groups were assessed by l.s.d. test, using SPSS software. In conclusion, Spin1 may be involved in metaphase arrest in oocyte and zygotic genome activation during early embryo development in pigs.

Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains

Histone H3K4 methylation is associated with active genes and, along with H3K27 methylation, is part of a bivalent chromatin mark that typifies poised developmental genes in embryonic stem cells (ESCs). However, its functional roles in ESC maintenance and differentiation are not established. Here we show that mammalian Dpy-30, a core subunit of the SET1/MLL histone methyltransferase complexes, modulates H3K4 methylation in vitro, and directly regulates chromosomal H3K4 trimethylation (H3K4me3) throughout the mammalian genome. Depletion of Dpy-30 does not affect ESC self-renewal, but significantly alters the differentiation potential of ESCs, particularly along the neural lineage. The differentiation defect is accompanied by defects in gene induction and in H3K4 methylation at key developmental loci. Our results strongly indicate an essential functional role for Dpy-30 and SET1/MLL complex-mediated H3K4 methylation, as a component of the bivalent mark, at developmental genes during the ESC fate transitions.

Structural basis for H3K4 trimethylation by yeast Set1/COMPASS

Histone methylation on lysine 4 of histone H3 (H3K4) is a hallmark of activity of the transcribed regions on eukaryotic chromatin. H3K4 can be mono-, di- and trimethylated by Set1/COMPASS. In this review, we will discuss recent findings regarding the role of the Y/F switch by the catalytic domain of Set1 in the regulation of H3K4 methylation by Set1/COMPASS.

Specific Lysine Sites in Histone H3 Contribute To Spurious Transcription

Transcriptional co‐factors including histone modifying enzymes regulate gene expression at both initiation and elongation stages of transcription. Recent studies demonstrate that Set2‐catalyzed histone H3K36 methylation serves as a signal for recruitment of histone deacetylase Rpd3 Small complex that decreases histone acetylation in coding regions and inhibits aberrant initiation of transcription from cryptic promoters within the coding region of certain genes. In this study, we investigated the possible roles of individual lysine sites in histones H3 and H4 in spurious transcription initiation by Northern blotting, chromatin immunoprecipitation and quantitative RT‐PCR. Our results indicate that H3K4 methylation, H3K14 and H3K23 acetylation specifically contribute to aberrant transcription initiation in the absence of Set2. H3K4 mutation synergistically enhances the suppression of cryptic transcription initiation by H3K14 and H3K23 mutations in set2 deletion. In addition, the functions of these three lysine sites in H3 in transcription initiation are regulated by a number of proteins including Ccr4‐Not complex, Set1 and Spt3 that participate in regulation of H3K4 methylation and histone H3 acetylation, suggesting a complex regulating network exists in cryptic transcription initiation. Our study reveals new roles for these three histone lysines in H3.

Ubp8p, a Histone Deubiquitinase Whose Association with SAGA Is Mediated by Sgf11p, Differentially Regulates Lysine 4 Methylation of Histone H3 In Vivo

Despite recent advances in characterizing the regulation of histone H3 lysine 4 (H3-K4) methylation at the GAL1 gene by the H2B-K123-specific deubiquitinase activity of Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase)-associated Ubp8p, our knowledge on the general role of Ubp8p at the SAGA-dependent genes is lacking. For this study, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay, we have analyzed the role of Ubp8p in the regulation of H3-K4 methylation at three other SAGA-dependent yeast genes, namely, PHO84, ADH1, and CUP1. Like that at GAL1, H3-K4 methylation is increased at the PHO84 core promoter in the UBP8 deletion mutant. We also show that H3-K4 methylation remains invariant at the PHO84 open reading frame in the Deltaubp8 mutant, demonstrating a highly localized role of Upb8p in regulation of H3-K4 methylation at the promoter in vivo. However, unlike that at PHO84, H3-K4 methylation at the two other SAGA-dependent genes is not controlled by Ubp8p. Interestingly, Ubp8p and H3-K4 methylation are dispensable for preinitiation complex assembly at the core promoters of these genes. Our ChIP assay further demonstrates that the association of Ubp8p with SAGA is mediated by Sgf11p, consistent with recent biochemical data. Collectively, the data show that Ubp8p differentially controls H3-K4 methylation at the SAGA-dependent promoters, revealing a complex regulatory network of histone methylation in vivo.

Histone H3 Lysine 4 Mono-methylation does not Require Ubiquitination of Histone H2B

The yeast Set1-complex catalyzes histone H3 lysine 4 (H3K4) methylation. Using N-terminal Edman sequencing, we determined that 50% of H3K4 is methylated and consists of roughly equal amounts of mono, di and tri-methylated H3K4. We further show that loss of either Paf1 of the Paf1 elongation complex, or ubiquitination of histone H2B, has only a modest effect on bulk histone mono-methylation at H3K4. Despite the fact that Set1 recruitment decreases in paf1delta cells, loss of Paf1 results in an increase of H3K4 mono-methylation at the 5' coding region of active genes, suggesting a Paf1-independent targeting of Set1. In contrast to Paf1 inactivation, deleting RTF1 affects H3K4 mono-methylation at the 3' coding region of active genes and results in a decrease of global H3K4 mono-methylation. Our results indicate that the requirements for mono-methylation are distinct from those for H3K4 di and tri-methylation, and point to differences among members of the Paf1 complex in the regulation of H3K4 methylation.