Unconventional structure and function of PHD domains from Additional Sex Combs-like proteins

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Abstract

The Polycomb Repressive-Deubiquitinase (PR-DUB) complex removes ubiquitin from Lysine residue 119 on histone H2A (H2AK119Ub) in humans. The PR-DUB is composed of two central protein factors, the catalytic Breast Cancer type 1 susceptibility protein (BRCA1)-activating protein 1 (BAP1), and one of Additional Sex Combs-like 1–3 (ASXL1–3). A Plant Homeodomain (PHD) at the C-terminus of ASXL proteins is recurrently truncated in cancer, and was previously proposed to recognise epigenetic modifications on the N-terminal tail of histone H3. Here we demonstrate that the ASXL PHD domain lacks features required for histone tail recognition and is unable to bind histone H3 epigenetic marks. Modelling the structure of the ASXL PHD using AlphaFold3 suggests that the domain has an atypical fold and that the isolated ASXL PHD can chelate a single Zinc ion in vitro , compared to the two ions conventionally bound by PHD domains. Recently, the ASXL PHD was shown to bind an auxiliary set of PR-DUB interactors, named methyl CpG-binding domain proteins 5 (MBD5) and 6 (MBD6). We show that the ASXL PHD-MBD5 and -MBD6 complexes are stable in vitro, and surprisingly contain a composite Zinc-binding site at the interface between the two proteins. Overall, this data suggests an unconventional pairing of domains coordinate key functions of the PR-DUB — a non-canonical PHD domain from ASXL proteins obligately partners with MBD5 and 6, which were themselves misannotated because they cannot bind to methylated DNA.

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    Referee #2

    Evidence, reproducibility and clarity

    Critique

    In this manuscript, the authors examine the biochemistry of two protein domains that are, on the basis of sequence similarity, predicted to function autonomously as binders of histone H3 tails or methylated DNA. They present solid data to suggest that neither domain in fact has this function, but that they act as protein interaction domains that form a heterodimer mediated by the presence of a zinc ion (two ligands from each protein).

    In the first part of the Results, the authors note that ASXL PHD doesn't contain aromatics that are characteristic of methylated lysine binding. I would just note that they don't mention at …

  3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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    Referee #1

    Evidence, reproducibility and clarity

    Summary: The Polycomb Repressive-Deubiquitinase (PR-DUB) complex catalyzes histone H2AK119Ub deubiquitinylation, regulating gene expression and chromatin dynamics. It comprises the BAP1 deubiquitinylase and one of three ASXL proteins (ASXL1-3). ASXL proteins contain a highly conserved C-terminal Plant Homeodomain (PHD), which was proposed to recognize epigenetic marks on histone H3 tail and other proteins. Mutations and truncations in the PHD domain are frequently observed in cancer. The authors propose that the ASXL PHD domain does not target histone H3 PTM marks. They model the PHD domain using AlphaFold3 and identified a …