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Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross-links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model of WDR76 and SPIN1 bound to the nucleosome. [ABSTRACT FROM AUTHOR]

Increasing incidence of Fragile X disorders (FXD) and of immune-mediated disorders in FXD suggests that additional factors besides FMR1 mutations contribute to the pathogenesis. Here, we discovered that the expression levels or splicing of specific transposon element (TE)-derived genes, regulating purine metabolism and immune responses against viral infections are altered in FXD. These genes include HLA genes clustered in chr6p21.3 and viral responsive genes in chr5q15. Remarkably, these TE-derived genes contain a low A T/C G suggesting base substitutions of A T to C G. The TE-derived genes with changed expression levels contained a higher content of 5'-CG-3' dinucleotides in FXD compared to healthy donors. This resembles the genomes of some RNA viruses, which maintain high contents of CG dinucleotides to sustain their latent infection exploiting antiviral responses. Thus, past viral infections may have persisted as TEs, provoking immune-mediated disorders in FXD., (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Molecular Medicine.)

WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response., Teaser: In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.