Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin

Abstract

Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. We show that DPY30 binding to ASH2L leads to stabilization and integration of ASH2L IDRs into the MLL1 complex and establishes new ASH2L-NCP contacts. The significance of ASH2L-DPY30 interactions is demonstrated by requirement of both ASH2L IDRs and DPY30 for dramatic increase of processivity and activity of the MLL1 complex. This DPY30 and ASH2L-IDR dependent regulation is NCP-specific and applies to all members of the MLL/SET1 family of enzymes. We further show that DPY30 is causal for de novo establishment of H3K4me3 in ESCs. Our study provides a paradigm of how H3K4me3 is regulated on chromatin and how H3K4me3 heterogeneity can be modulated by ASH2L IDR interacting proteins.

An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability

“…At 50 mM NaCl, we observed no compelling difference in MLL1C binding between any of these nucleosomes ( Figure 2C ). This finding agreed with structural studies where binding between MLL1C and the nucleosome occurs primarily through interactions with nucleosomal DNA and, to a lesser degree, the H4 N-terminal tail (Lee et al, 2021; Park et al, 2019). Thus, the increased H3K4 methylation observed when the H3 N-terminal tail was acetylated was not due to enhanced MLL1C – nucleosome binding.…”

“…Because of the low level of enzymatic activity towards the unacetylated nucleosomes we could not make a statistically significant comparison between the Hill and Michaelis-Menten fits. There have been limited studies of MLL1C activity on nucleosomes (Park et al, 2019;Patel et al, 2011;Xue et al, 2019), so an overlooked potential allostery is understandable given the complex possible interactions between this enzyme and substrate (Lee et al, 2021;Park et al, 2019) Interestingly, although overall kcat was ~17-fold greater for the H3tri ac nucleosomes, the K0.5 values (substrate concentration at half-maximal velocity/half-saturation for an allosterically regulated enzyme) were indistinguishable (Table 1). Therefore, although MLL1C catalytic efficiency toward H3tri ac nucleosomes was enhanced by an increase in kcat, this catalytic efficiency was not driven by K0.5, which suggested no increase in relative binding affinity.…”

Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome

“…The loop extends over 40 Å on the periphery of the SPRY domain to the nucleosomal DNA and contains an anti-parallel beta sheet comprising residues 415-419 and 424-428 (Figure 4c). This positions K419 and K421 near the DNA, consistent with the deleterious effect of substitution of these residues on DPY30-dependent methylation by MLL1 (3). This fit satisfies eight crosslinks, including two inter-subunit crosslinks between Ash2L residue K437 and MLL1 residues K3870 and 3873 (Figure 4c).…”

“…The proximity of the Ash2L IDR and SPRY-insertion region to nucleosomal DNA in our model (Figure 4a), could account for the importance of DPY30 binding to MLL1-WRAD activity. Previous studies have shown that DPY30 greatly increases MLL1 methyltransferase activity on nucleosomes and that this increase in activity depends upon the Ash2L IDR (3). DPY30 forms multiple contacts with the IDR and the SDI helix, which help to stabilize folding of the IDR, as supported by NMR studies(3).…”

“…This observation is consistent with a role for DPY30 in favoring binding between SHL6 and SHL7, as observed in structures of the complete MLL1-WRAD complex containing DPY30 (6KIV, 6KIX, 6KIZ, 6PWV and this work). DPY30 likely exerts its effect through its interactions with the Ash2L IDR, which undergoes conformational changes in the presence of DPY30 as reflected in changes in NMR spectra (3).…”