Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators

The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment

“…It was hypothesised that the N-terminal region contains a ubiquitylation-dependent recruitment motif (UDR; Weinberg et al, 2021) and we show that this maps to 164-219 of DNMT3A1, integrating both ubiquitin recognition as well as our nucleosome interaction region (Fig 5A). Intriguingly, this region is found to be highly invariant in the normal population, based on the absence of missense variants found in the gnomAD population database (Fig 4B;Deak & Cook, 2022;Karczewski et al, 2020). This underlines the importance of the DNMT3A1 nucleosome and ubiquitin interacting region during normal development and agrees with a recent mouse study showing the necessity of the N-terminal region of DNMT3A1 for postnatal neural development (Gu et al, 2022).…”

“…Missense variant analysis was performed as described before (Deak & Cook, 2022). Briefly, data on missense variants associated with the human DNMT3A1 gene (transcript ENST00000264709.3, genome build GRCh37 / hg19) were retrieved from the gnomAD v2.1.1 dataset (Karczewski et al ., 2020).…”

“…Briefly, data on missense variants associated with the human DNMT3A1 gene (transcript ENST00000264709.3, genome build GRCh37 / hg19) were retrieved from the gnomAD v2.1.1 dataset (Karczewski et al ., 2020). Plot Protein Converter (Deak & Cook, 2022) was used to filter the data for non-deleterious variants and format it for the Plot Protein program (Turner, 2013), enabling visualisation of variants on the DNMT3A1 protein sequence.…”

Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome

“…Primary sequence analysis Domain boundaries of SALL proteins were identified based on UniProt annotations (Gasteiger et al, 2005) and previous sequence analyses (Pantier et al, 2021). Missense mutations from gnomAD were processed using 1D-3D and VdVp_calculator scripts (Deak & Cook, 2022). For SALL4, missense variants categorised as "pathogenic" or of "uncertain significance" were extracted from ClinVar.…”

“…To further understand the contribution of different SALL4 domains to function, we extracted population missense mutations and calculated an overall missense depletion score for SALL4 protein (Vp) of 0.38 (Deak & Cook, 2022) (Fig 1A). We then considered individual domains of SALL4 and calculated missense depletion relative to the whole protein (VdVp ratio), where a score of ≥1 would indicate that a single domain is not depleted of missense variants compared with the full protein sequence (Deak & Cook, 2022). Three regions were observed to be comparatively depleted of population missense mutations: the N-terminal NuRD binding motif (Lauberth & Rauchman, 2006) (VdVp = 0.22); a glutamine-rich (Q-rich) sequence that has been reported to participate in SALL protein homo-and heterodimer formation (VdVp = 0.50) (Sweetman et al, 2003); and ZFC4, which is essential for SALL4 function in mice (VdVp = 0.47) (Pantier et al, 2021) (Fig 1A).…”