PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing
336
Citation
52
Reference
10
Related Paper
Citation Trend
Keywords:
Histone Methylation
Cite
Although post-translational modifications (-PTMs) of some histone H3 lysine residues are well studied, the PTMs of histone H3 lysine 37 in mammalian cells remain largely unknown. In this study, we provide evidence to show that SMYD family member 5 (SMYD5) is a histone H3-specfic methyltransferase that catalyzes mono-methylation of H3 lysine 36 and 37 (H3K36/K37me1) in vitro. The site-mutagenesis analysis shows that a species-conserved histidine in its catalytic SET domain is required for its histone methyltransferase activity. Genetic deletion of Smyd5 in murine embryonic stem cells (mESCs) partially reduces the global histone H3K37me1 level in cells, suggesting SMYD5 is one of histone methyltransferases catalyzing histone H3K37me1 in vivo. Hence, our study reveals that SMYD5 is a histone H3-specific methyltransferase that mediates histone H3K36/K37me1, which provides a biochemical basis for further studying its functions in mammalian cells.
Histone Methylation
Histone octamer
Histone code
Cite
Citations (9)
Histone Methylation
Heterochromatin protein 1
Histone code
Cite
Citations (515)
Histone H3 lysine 36 (H3K36) methylation was identified as a conserved modification from yeast to human. In yeast, biochemical characterization of the SET2 protein and genome wide mapping of H3K36me2 and K36me3 indicate that H3K36 methylation functions in transcription elongation through Set2/Rpd3S pathway.
A number of H3K36 methyltransferases and demethylases have been identified in different species, which underscores the dynamics of H3K36 methylation. As in yeast, H3K36me3 also peaks at the 3’ end of genes in mammals. The genome wide view of H3K36me1 and H3K36me2 is not clear yet. To date, the functional significance of H3K36 methylation remains largely unknown in mammals.
In this thesis, homologs of SET2 in mammals, including Nsd1, Nsd2, Nsd3, and HypB, were studied. Nsd proteins displayed weak methyltransferase activity towards histone H3 in vitro. Their target specificities needs to be further analyzed. In vitro, HypB showed strong activity for histone H3 lysine 36. In vivo, H3K36 trimethylation levels were significantly reduced in HypB knock-down cells, indicating that HypB is a major H3K36 trimethyltransferase. Distribution of H3K36 methylation (mono-, di-, and tri-) were analyzed by immunofluorescence both in human and mouse cells. All three methylation states of showed euchromatic distribution, whereas H3K36 mono- and dimethylation also showed heterochromatic enrichment in terminally differentiated NIH3T3 cells as well. In embryonic stem cells, H3K36 methylation showed an inverse correlation with the expression level of Oct4, a stem cell marker, suggesting a potential role of H3K36 methylation in ES cell differentiation. After induction of differentiation by removing LIF or adding retinoic acid to the culture medium, stem cell genes failed to be repressed and lineage specific genes failed to be activated to the same degree in HypB knockdown cell as observed in mock treated ES cells. The presence of H3K36me3 along Oct4 locus was mapped by CHIP. H3K36me3 was highly enriched in the coding region, and was low upstream of the transcription start site in undifferentiated ES cells. During differentiation, however, H3K36me3 decreased on the coding region and increased slightly on enhancer region of Oct4 in the course of Oct4 repression after differentiation. In all, we propose that H3K36me3 is catalyzed by HypB and has an inverse correlation with Oct4 expression. HypB facilitates ES cell differentiation. The molecular mechanism by which HypB facilitates differentiation requires further investigation.
Histone Methylation
Cite
Citations (0)
Presentation (obstetrics)
Cite
Citations (180)
Covalent modification of histone tails is crucial for transcriptional regulation, mitotic chromosomal condensation, and heterochromatin formation. Histone H3 lysine 9 (H3-K9) methylation catalyzed by the Suv39h family proteins is essential for establishing the architecture of pericentric heterochromatin. We recently identified a mammalian histone methyltransferase (HMTase), G9a, which has strong HMTase activity towards H3-K9 in vitro. To investigate the in vivo functions of G9a, we generated G9a -deficient mice and embryonic stem (ES) cells. We found that H3-K9 methylation was drastically decreased in G9a -deficient embryos, which displayed severe growth retardation and early lethality. G9a -deficient ES cells also exhibited reduced H3-K9 methylation compared to wild-type cells, indicating that G9a is a dominant H3-K9 HMTase in vivo. Importantly, the loss of G9a abolished methylated H3-K9 mostly in euchromatic regions. Finally, G9a exerted a transcriptionally suppressive function that depended on its HMTase activity. Our results indicate that euchromatic H3-K9 methylation regulated by G9a is essential for early embryogenesis and is involved in the transcriptional repression of developmental genes.
Euchromatin
Histone Methylation
Heterochromatin protein 1
Cite
Citations (1,187)
A novel histone methyltransferase, termed Set9, was isolated from human cells. Set9 contains a SET domain, but lacks the pre- and post-SET domains. Set9 methylates specifically lysine 4 (K4) of histone H3 (H3-K4) and potentiates transcription activation. The histone H3 tail interacts specifically with the histone deacetylase NuRD complex. Methylation of histone H3-K4 by Set9 precludes the association of NuRD with the H3 tail. Moreover, methylation of H3-K4 impairs Suv39h1-mediated methylation at K9 of H3 (H3-K9). The interplay between the Set9 and Suv39h1 histone methyltransferases is specific, as the methylation of H3-K9 by the histone methyltransferase G9a was not affected by Set9 methylation of H3-K4. Our studies suggest that Set9-mediated methylation of H3-K4 functions in transcription activation by competing with histone deacetylases and by precluding H3-K9 methylation by Suv39h1. Our results suggest that the methylation of histone tails can have distinct effects on transcription, depending on its chromosomal location, the combination of posttranslational modifications, and the enzyme (or protein complex) involved in the particular modification.
Histone Methylation
Histone code
Heterochromatin protein 1
Cite
Citations (555)
Histone Methylation
Histone code
Epigenomics
Histone octamer
Heterochromatin protein 1
Cite
Citations (12)
Gene expression within the context of eukaryotic chromatin is regulated by enzymes that catalyze histone lysine methylation. Histone lysine methyltransferases that have been identified to date possess the evolutionarily conserved SET or Dot1-like domains. We previously reported the identification of a new multi-subunit histone H3 lysine 4 methyltransferase lacking homology to the SET or Dot1 family of histone lysine methyltransferases. This enzymatic activity requires a complex that includes WRAD (WDR5, RbBP5, Ash2L, and DPY-30), a complex that is part of the MLL1 (mixed lineage leukemia protein-1) core complex but that also exists independently of MLL1 in the cell. Here, we report that the minimal complex required for WRAD enzymatic activity includes WDR5, RbBP5, and Ash2L and that DPY-30, although not required for enzymatic activity, increases the histone substrate specificity of the WRAD complex. We also show that WRAD requires zinc for catalytic activity, displays Michaelis-Menten kinetics, and is inhibited by S-adenosyl-homocysteine. In addition, we demonstrate that WRAD preferentially methylates lysine 4 of histone H3 within the context of the H3/H4 tetramer but does not methylate nucleosomal histone H3 on its own. In contrast, we find that MLL1 and WRAD are required for nucleosomal histone H3 methylation, and we provide evidence suggesting that each plays distinct structural and catalytic roles in the recognition and methylation of a nucleosome substrate. Our results indicate that WRAD is a new H3K4 methyltransferase with functions that include regulating the substrate and product specificities of the MLL1 core complex.
Histone Methylation
Histone code
Histone octamer
Cite
Citations (79)
Histone H3 lysine 4 (K4) methylation is a prevalent mark associated with transcription activation and is mainly catalyzed by the MLL/SET1 family histone methyltransferases. A common feature of the mammalian MLL/SET1 complexes is the presence of three core components (RbBP5, Ash2L and WDR5) and a catalytic subunit containing a SET domain. Unlike most other histone lysine methyltransferases, all four proteins are required for efficient H3 K4 methylation. Despite extensive efforts, mechanisms for how three core components regulate MLL/SET1 methyltransferase activity remain elusive. Here we show that a heterodimer of Ash2L and RbBP5 has intrinsic histone methyltransferase activity. This activity requires the highly conserved SPRY domain of Ash2L and a short peptide of RbBP5. We demonstrate that both Ash2L and the MLL1 SET domain are capable of binding to S-adenosyl-L- [methyl-(3)H] methionine in the MLL1 core complex. Mutations in the MLL1 SET domain that fail to support overall H3 K4 methylation also compromise SAM binding by Ash2L. Taken together, our results show that the Ash2L/RbBP5 heterodimer plays a critical role in the overall catalysis of MLL1 mediated H3 K4 methylation. The results we describe here provide mechanistic insights for unique regulation of the MLL1 methyltransferase activity. It suggests that both Ash2L/RbBP5 and the MLL1 SET domain make direct contacts with the substrates and contribute to the formation of a joint catalytic center. Given the shared core configuration among all MLL/SET1 family HMTs, it will be interesting to test whether the mechanism we describe here can be generalized to other MLL/SET1 family members in the future.
Histone Methylation
Cite
Citations (112)