Missense variants reveal functional insights into the human ARID family of gene regulators

Abstract

Missense variants are alterations to protein coding sequences that result in amino acid substitutions. They can be deleterious if the amino acid is required for maintaining structure or/and function, but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population can mirror the effects of negative selection on protein structure and function, such that functional sites on proteins are often depleted of missense variants. Advances in high-throughput sequencing have dramatically increased the sample size of available human variation data, allowing for population-wide analysis of selective pressures. In this study, we developed a convenient set of tools, called 1D-to-3D, for visualizing the positions of missense variants on protein sequences and structures. We used these tools to characterize human homologues of the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to characterise sites important for protein-protein interactions, histone modification recognition, and DNA binding by the ARID proteins. We find that comparing missense depletion patterns among paralogs can reveal sub-functionalization at the level of domains. We propose that visualizing missense variants and their depletion on structures can serve as a valuable tool for complementing evolutionary and experimental findings.

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

“…This is consistent with the finding that SALL4 haploinsufficiency is responsible for an autosomal dominant disorder. 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 and Cook 2022) (Fig. 1a).…”

“…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 to the full protein sequence (Deak and Cook 2022). Three regions were observed to be comparatively depleted of population missense mutations: the N-terminal NuRD binding motif (Lauberth and 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, Smith et al 2003); and ZFC4, which is essential for SALL4 function in mice (VdVp=0.47) (Pantier, Chhatbar et al 2021)(Fig.…”

“…Domain boundaries of SALL4 were identified based on UniProt annotations and previous sequence analyses (Pantier, Chhatbar et al 2021). Missense mutations from gnomAD were processed using 1D-to-3D and VdVp_calculator scripts (Deak and Cook 2022) and plotted using Plot Protein (Turner 2013).…”

“…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 to the full protein sequence (Deak and Cook 2022).…”