NTR: [histone H3-K27 methyltransferase allosteric activator activity]

[krchristie]

Please provide as much information as you can:

• Suggested term label: histone H3-K27 methyltransferase activator activity

• Definition (free text) def: "Binds to and increases the activity of a histone H3-K27 methyltransferase, an enzyme which catalyzes the transfer of a methyl group to lysine 27 of histone H3 (H3K27). [GOC:krc, PMID:15916951, PMID:17997413]

• Reference, in format PMID:####### (REQUIRED) PMID:15916951 - Montgomery ND, et al. 2005. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr Biol. 15(10):942-7 PMID:17997413 - Montgomery ND, et al. 2007. Molecular and functional mapping of EED motifs required for PRC2-dependent histone methylation. J Mol Biol. 374(5):1145-57

• Gene product name and ID to be annotated to this term mouse Eed

• Parent term(s) Equivalence axiom:

  intersection_of: GO:0140677 ! molecular function activator activity
  intersection_of: directly_positively_regulates GO:0044017 ! histone H3-K27 methyltransferase activity

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term? NA

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED) synonym: "histone H3-K27 methyltransferase stimulator activity" EXACT [GOC:krc]

• Cross-references

• For enzymes, please provide RHEA and/or EC numbers.

• Can also provide MetaCyc, KEGG, Wikipedia, and other links.

• Any other information

[pgaudet]

HI @krchristie

I looked at this with @colinlog , and he notes that EED is a core subunit of the complex, therefore it cannot act as a regulator. Since it's a core subunit, it's not surprising that it would be required for the activity of the histone methylase. EED's activity is rather a scaffold; right now we don't have any term more specific than the top-level of that branch, protein-macromolecule adaptor activity. I suggest you use this with the appropriate input(s).

I hope this works for you.

[krchristie]

HI @krchristie

I looked at this with @colinlog , and he notes that EED is a core subunit of the complex, therefore it cannot act as a regulator. Since it's a core subunit, it's not surprising that it would be required for the activity of the histone methylase. EED's activity is rather a scaffold; right now we don't have any term more specific than the top-level of that branch, protein-macromolecule adaptor activity. I suggest you use this with the appropriate input(s).

I hope this works for you.

Actually, I don't think this does work very well.

I keep finding that the lack of specific terms in MF is going to mean that enrichment analyses will become meaningless. I think we need MF terms that provide some level of specificity with respect to what the gene product is doing. Only putting the specificity in the inputs doesn't provide much information unless the inputs are actually displayed on websited, used in enrichment analyses, etc.

@vanaukenk - Can we discuss this type of issue an at annotation call, probably in the fall once the summer vacations are over.

[ValWood]

I'm semi-agnostic as to whether we include the specific terms. However, this shouldn't affect enrichments because enrichments work on gene sets of a significant number of members (i.e. pathways), and the regulator terms are leaf nodes with single annotations or a couple at most. We need to annotate to the process(pathway) i.e. GO:0045815 transcription initiation-coupled chromatin remodeling or whatever, to enable enrichments. To illustrate you will notice that MF terms other than 'protein binding' or occasionally transcription regulators never appear in enrichments (and when they do, there should always be a more informative process enriched).

I can see the advantage for users to see the precise term label without having to read the substrate and a disadvantage for GO editors to replicate all of the functions that require specific regulators in the "regulator branch". so it is a useful discussion to have.

[krchristie]

I'm semi-agnostic as to whether we include the specific terms. However, this shouldn't affect enrichments because enrichments work on gene sets of a significant number of members (i.e. pathways), and the regulator terms are leaf nodes with single annotations or a couple at most. We need to annotate to the process(pathway) i.e. GO:0045815 transcription initiation-coupled chromatin remodeling or whatever, to enable enrichments. To illustrate you will notice that MF terms other than 'protein binding' or occasionally transcription regulators never appear in enrichments (and when they do, there should always be a more informative process enriched).

I agree that the leaf nodes themselves aren't the terms that will show up in enrichments, but I think that representing the MF with something as non-specific as "protein-macromolecule adaptor activity" is not going to be useful. If we create specific MF terms then we will likely also have a structure of terms such that there could some intermediate term that does become enriched and provides more information that just "protein-macromolecule adaptor activity"

I can see the advantage for users to see the precise term label without having to read the substrate and a disadvantage for GO editors to replicate all of the functions that require specific regulators in the "regulator branch". so it is a useful discussion to have.

Most interfaces do not display the extension/input in a user friendly way. In addition, it seems that the GO editors have decided that we need to represent the mechanistic aspects of functions with MF terms. If that's the decision, it seems that we need to have meaningful MF terms. I feel that replacing the obsoleted BP term that provided very specific information that allowed users to see immediately that it Eed is involved in histone H3K27 methylation with such a vague MF term as "protein-macromolecule adaptor activity" is not a user friendly change (follow red arrow in pic).

[krchristie]

HI @krchristie

I looked at this with @colinlog , and he notes that EED is a core subunit of the complex, therefore it cannot act as a regulator. Since it's a core subunit, it's not surprising that it would be required for the activity of the histone methylase. EED's activity is rather a scaffold; right now we don't have any term more specific than the top-level of that branch, protein-macromolecule adaptor activity. I suggest you use this with the appropriate input(s).

Hi @pgaudet,

I've read several reviews on PRC2 now. Three of the best are listed below along with some key quotes that discuss the high level of taxonomic conservation of the structure and the allosteric mechanism of action within the PRC2 catalytic core.

In summary, EZH2, the "catalytic" subunit of PRC2, is NOT functional in the absence of being assembled into the trimeric catalytic core containing EZH2, EED, and SUZ12 (specifically the VEFS domain of SUZ12). When EED or SUZ12 bind appropriate histone modifications, they allosterically change the shape of the catalytic pocket of EZH2. The experts describe these proteins as allosteric activators of H3K27 methylation REQUIRED for activation of the catalytic pocket of the EZH2 subunit of the PRC2 catalytic core, NOT as passive "scaffold" proteins.

Thus, to say that EED "cannot act as a regulator" because it "is a core subunit of the complex" and that "EED's activity is rather a scaffold" is entirely counter to how the activity of this subunit is described by the experts who study the PRC complex. It seems that your rule that a subunit of the complex cannot regulate the catalytic subunit's activity does not accurately reflect the biology described by the experts on PRC2.

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From these reviews, I would currently modify my term request for an MF term for Eed to something like what I've put below. It's possible that this term is broad enough to cover the allosteric activation activity that VEFS domain of SUZ12 possesses, however, it may be more appropriate to have different terms depending on what marks they bind. I would need to do more reading to understand the allosteric activitation activity of SUZ12.

Suggested term label: histone H3-K27 methyltransferase allosteric activator activity

Definition (free text) def: Binds to a repressive chromatin mark, including H3-K27me3, H3-K9me3, or H4-K20me3, and allosterically changes the configuration of the catalytic histone H3-K27 methyltransferase subunit such that the catalytic site is activated, enabling the enzyme to catalyze the transfer of a methyl group to lysine 27 of histone H3 (H3K27). [GOC:krc, PMID:15916951, PMID:17997413, PMID:33232890, PMID:31708574, PMID:22349693]

Reference, in format PMID:####### (REQUIRED) PMID:15916951 - Montgomery ND, et al. 2005. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr Biol. 15(10):942-7 PMID:17997413 - Montgomery ND, et al. 2007. Molecular and functional mapping of EED motifs required for PRC2-dependent histone methylation. J Mol Biol. 374(5):1145-57 PMID:33232890 - Glancy E, et al. 2021. Structural basis for PRC2 engagement with chromatin. Curr Opin Struct Biol. 2021 Apr;67:135-144. PMID:31708574 - Chammas P, et al. 2020. Engaging chromatin: PRC2 structure meets function. Br J Cancer. 122(3):315-328. PMID:22349693 - O'Meara MM & Simon JA. 2012. Inner workings and regulatory inputs that control Polycomb repressive complex 2. Chromosoma. 2012 Jun;121(3):221-34.

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Chammas P, Mocavini I, Di Croce L. 2020. Engaging chromatin: PRC2 structure meets function. Br J Cancer. 122(3):315-328. PMID:31708574

• The PRC2 core comprises three stoichiometric factors: enhancer of Zeste (EZH)1 or EZH2, which has a SET domain and is the catalytic subunit of the complex (7,21); suppressor of Zeste (SUZ) 12; and embryonic ectoderm development (EED) (Table 1). These three proteins form the minimal core that confers histone methyltransferase (HMT) activity.

• The assembly of the trimeric core is essential for HMT activity: in isolation, EZH2 adopts an autoinhibited conformation, with the post-SET domain (the region C-terminal to the SET domain) folded upwards into the lysine-binding cleft, blocking the substrate from engaging the active site.31–33

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Glancy E, Ciferri C, Bracken AP. 2021. Structural basis for PRC2 engagement with chromatin. Curr Opin Struct Biol. 2021 Apr;67:135-144. PMID:33232890

• The core members of PRC2 directly engage with chromatin via interactions with histone tails [35–38] and DNA [39,40]. Initial studies revealed that core PRC2 member EED binds to H3K27me3 and this interaction allosterically promotes PRC2 histone methyltransferase (HMT) activity [34,36,41]. The structural basis for this allosteric activation was initially described in fungi (Chaetomium thermophilum) by X-ray crystallography [35]. This revealed that the stabilisation of the EZH2–SRM domain is a key defining characteristic towards the achievement of a stimulated state [35]. The structural organisation within core PRC2 and its allosteric activation have been comprehensively reviewed previously [42,43].

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O'Meara MM & Simon JA. 2012. Inner workings and regulatory inputs that control Polycomb repressive complex 2. Chromosoma. 2012 Jun;121(3):221-34. PMID:22349693

Inputs to EZH2 from core partner subunits

• Among characterized SET domain proteins, there is a continuum ranging from those that can function as lysine methyltransferases on their own to those that require assembly into multiprotein complexes. At one extreme, the viral SET (vSET) protein is an active HMTase that consists essentially of an isolated SET domain (Qian et al. 2006). PRC2 lies at the other extreme, with its three noncatalytic core subunits required to stimulate activity, particularly the two (EED and SUZ12) that directly contact EZH2 (Fig. 1a). .... [snip] .... Indeed, recent work has revealed allosteric input of the EED subunit to PRC2 enzyme activity (see below).

• The EED top pocket, featuring a conserved aromatic cage, is configured for preferential binding to repressive chromatin marks, including H3-K27me3, H3-K9me3, and H4-K20me3, as opposed to “activating” marks such as H3-K4me3. This discrimination relies on residues flanking the methylatable lysine, thereby exploiting the ARKS motifs at repressive positions K9 and K27. PRC2 binding to tri-methylated H3 peptides boosts its HMTase activity, with the H3-K27me3 peptide delivering the most robust stimulation (Margueron et al. 2009; Xu et al. 2010). Thus, EED harbors a site for allosteric PRC2 stimulation via binding the H3-K27me3 reaction product. Importantly, this may provide a mechanism to maintain or propagate H3-K27 methylation in chromatin regions where this repressive mark pre-exists (Hansen et al. 2008; Margueron et al. 2009).

[ValWood]

that EED is a core subunit of the complex, therefore it cannot act as a regulator.

Aside: Is that a rule? We have lots of enzyme regulators that are core subunits of the complex?

dolichol-phosphate-mannose synthase complex (GO:0033185) RNA decapping complex (GO:0098745) NatA complex cyclin dependent kinases hundreds...

Is Colin's comment confusing MF regulator with "regulation of process"

[pgaudet]

Aside: Is that a rule? We have lots of enzyme regulators that are core subunits of the complex?

I also thought a regulator could be part of the core complex.

[pgaudet]

I think my comment above was intended a bit differently:

I looked at this with @colinlog , and he notes that EED is a core subunit of the complex, therefore it cannot act as a regulator.

We were proposing it's a scaffold; but not that because it's a core subunit, it cannot be a regulator.

[deustp01]

We were proposing it's a scaffold; but not that because it's a core subunit, it cannot be a regulator.

Even then, do we want these exclusive categories, e.g., a gene product can only ever enable one thing, so a structural component cannot also be a regulator cannot also enable whatever the function of the complex is?