Differential complex formation via paralogs in the human Sin3 protein interaction network

Abstract

Despite the continued analysis of HDAC inhibitor efficacy in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The functional attributes of these protein complexes remain poorly characterized in humans. Contributing to the poor definition of Sin3 complex attributes in higher eukaryotes is the presence of two Sin3 scaffolding proteins, SIN3A and SIN3B. Here we show that paralog switching influences the interaction networks of the Sin3 complexes. While SIN3A and SIN3B do have unique interaction network components, we find that SIN3A and SIN3B interact with a common set of proteins.Additionally, our results suggest that SIN3A and SIN3B may possess the capacity to form hetero-oligomeric complexes. While one principal form of SIN3B exists in humans, the analysis of rare SIN3B proteoforms provides insight into the domain organization of SIN3B. Together, these findings shed light on the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.

Perturbation of BRMS1 interactome reveals pathways that impact cell migration

“…To more clearly look at the interactions of BRMS1 and BRMS1L in association with the Sin3/HDAC complexes, we utilized normalized spectral counts of previously published mass spectrometry data [24]. We found a distinct pattern difference of BRMS1 and BRMS1L binding with SIN3A and SIN3B ( Figure 2D ).…”

“…The BRMS1 primers listed in Supplementary Data were used to amplify a sequence coding for BRMS1 isoform 1 (NP_056214), or for mutant versions of BRMS1 as indicated in the figure legends, using a previously reported BRMS1 construct as a template [24]. A short synthetic duplex DNA oligonucleotide (described in Supplementary Data ) was used to clone a short fragment of the C terminus of BRMS1 (amino acids 230-246).…”

“…Cross-linking data were utilized from publicly available data published by Adams et. al 2020 [21]. The BRMS1 cross-links were visualized within the xiView platform [22].…”

Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry

“…Recent advances in XL-MS have introduced MS-cleavable crosslinkers, which generate distinct fragment pairs in MS2 and therefore substantially reduce the complexity of data analysis and improve identification accuracy (Matzinger & Mechtler, 2021). Disuccinimidyl sulfoxide (DSSO) (Kao et al, 2011) is the most extensively used MS-cleavable reagent, and has been applied to the characterisation of protein interactions both in isolated proteins as well as complex samples (Adams et al, 2020;Klykov et al, 2018;Nguyen et al, 2020;Ser et al, 2019;Smith et al, 2018;Wang et al, 2017).…”

Softly but surely: A new perspective on transcriptional repression

“…Further exploration is needed to better define the molecular bases for the differential impact of these complexes on the target genes they either silence or “softly repress.” For example, the Sin3 complex associates with different modules with specific chromatin‐modifying activities. [ 2 ] Could a discrete Sin3 complex arrangement underline its function in soft repression, while an alternative one directs silencing? Another question lies in the biological impact of these slight modulations of repression.…”