Abstract:Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H… Show more
“…The model structure of the MLL1 RWSAD -NCP complex (Fig. 1d) was built by rigid-body fitting and real space refinement using crystal structures of mouse RbBP5 (PDB ID: 5OV3) 27 , human WDR5 (PDB ID: 2H14) 28 , human MLL1 SET -ASH2L SPRY -RbBP5 330–375 (PDB ID: 5F6L) 16 , a DPY30 dimer (PDB ID: 6E2H) 29 , and the 601-NCP (PDB ID: 3MVD) 3 .Fig. 1Cryo-EM structure of the MLL1 RWSAD -NCP complex.…”
Section: Resultsmentioning
confidence: 99%
“…Three model structures of MLL1 RWSAD -NCP, RbBP5-NCP, and MLL1 RWS -NCP were subjected to the real-space refinement using PHENIX 66 after rigid-body fitting using Chimera 67 . Crystal structures of mouse RbBP5 (PDB ID: 5OV3) 27 , human WDR5 (PDB ID: 2H14) 28 , human MLL1 SET -ASH2L SPRY -RbBP5 330–375 (PDB ID: 5F6L) 16 , a DPY30 dimer (PDB ID: 6E2H) 29 , the 601-NCP (PDB ID: 3MVD) 3 , and the ASH2L IDR model structure from I-TASSER 34,35 were used for the rigid-body fitting and following real-space refinement. Validations of three model structures were performed by MolProbity 68 .…”
Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
“…The model structure of the MLL1 RWSAD -NCP complex (Fig. 1d) was built by rigid-body fitting and real space refinement using crystal structures of mouse RbBP5 (PDB ID: 5OV3) 27 , human WDR5 (PDB ID: 2H14) 28 , human MLL1 SET -ASH2L SPRY -RbBP5 330–375 (PDB ID: 5F6L) 16 , a DPY30 dimer (PDB ID: 6E2H) 29 , and the 601-NCP (PDB ID: 3MVD) 3 .Fig. 1Cryo-EM structure of the MLL1 RWSAD -NCP complex.…”
Section: Resultsmentioning
confidence: 99%
“…Three model structures of MLL1 RWSAD -NCP, RbBP5-NCP, and MLL1 RWS -NCP were subjected to the real-space refinement using PHENIX 66 after rigid-body fitting using Chimera 67 . Crystal structures of mouse RbBP5 (PDB ID: 5OV3) 27 , human WDR5 (PDB ID: 2H14) 28 , human MLL1 SET -ASH2L SPRY -RbBP5 330–375 (PDB ID: 5F6L) 16 , a DPY30 dimer (PDB ID: 6E2H) 29 , the 601-NCP (PDB ID: 3MVD) 3 , and the ASH2L IDR model structure from I-TASSER 34,35 were used for the rigid-body fitting and following real-space refinement. Validations of three model structures were performed by MolProbity 68 .…”
Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
“…The catalytic domain of SET1 is found at the junction of the Y-shaped complex and makes contacts with every subunit, except for Dpy-30 (Qu et al, 2018) (Figure 2A). Interestingly, the cryo-EM structure nicely explains the modest stimulatory functions of Dpy-30 on the MT activity of SET1 on peptides when the complex is assembled with purified components (Haddad et al, 2018). Clustering of the particles revealed two conformationally distinct complexes, suggesting that COMPASS is a structurally dynamic complex that can exist in at least two conformers likely helping COMPASS to adapt to the structurally dynamic environment of chromatin (Maeshima et al, 2019).…”
Section: Recognition Of H2b Ubiquitinated Ncp By Compassmentioning
Post-translational modifications (PTMs) of histone proteins play essential functions in shaping chromatin environment. Alone or in combination, these PTMs create templates recognized by dedicated proteins or change the chemistry of chromatin, enabling a myriad of nuclear processes to occur. Referred to as cross-talk, the positive or negative impact of a PTM on another PTM has rapidly emerged as a mechanism controlling nuclear transactions. One of those includes the stimulatory functions of histone H2B ubiquitylation on the methylation of histone H3 on K79 and K4 by Dot1L and COMPASS, respectively. While these findings were established early on, the structural determinants underlying the positive impact of H2B ubiquitylation on H3K79 and H3K4 methylation were resolved only recently. We will also review the molecular features controlling these cross-talks and the impact of H3K27 tri-methylation on EZH2 activity when embedded in the PRC2 complex.
“…An interpretation is that, in Dpy30 -KO chromatin, depletion of H3K4 methylation progresses through a H3K4me1 intermediate stage, and that loci highly enriched for H3K4me3 thus maintain enrichment for this mark for a longer period of time. An alternative, and not mutually exclusive, interpretation, is that new H3K4 methylation in these regions is less reliant on DPY30 38 .…”
SummaryHistone 3 lysine 4 trimethylation (H3K4me3) is associated with promoters of actively expressed genes, with genes important for cell identity frequently having exceptionally broad H3K4me3-enriched domains at their TSS. While H3K4 methylation is implicated in contributing to transcription, maintaining transcriptional stability, facilitating enhancer-promoter interactions, and preventing irreversible silencing, some studies suggest it has little functional impact. Therefore, the function of H3K4 methylation is not resolved. Insufficient insulin release by β-cells is the primary etiology in type 2 diabetes (T2D) and is associated with the loss of expression of genes essential to normal β-cell function. We find that H3K4me3 is reduced in islets from mouse models of diabetes and from human donors with T2D. Using a genetic mouse model to impair H3K4 methyltransferase activity of TrxG complexes, we find that reduction of H3K4 methylation significantly reduces insulin production and glucose-responsiveness and increases transcriptional entropy, indicative of a loss of β-cell maturity. Genes that are downregulated by reduction to H3K4 methylation are concordantly downregulated in T2D. Loss of H3K4 methylation causes global dilution of epigenetic complexity but does not generally reduce gene expression – instead, genes related to β-cell function and/or in particular chromatin environments are specifically affected. While neither H3K4me3 nor H3K4me1 are strictly required for the expression of many genes, the expression of genes with critical roles in β-cell function becomes destabilized, with increased variance and decreased overall expression. Our data further suggests that, in absence of H3K4me3, promoter-associated H3K4me1 is sufficient to maintain expression. Together, these data implicate H3K4 methylation dysregulation as destabilizing β-cell gene expression and contributing to β-cell dysfunction in T2D.
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