Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components

Abstract

Over millions of years, eukaryotes evolved from unicellular to multicellular organisms with increasingly complex genomes and sophisticated gene expression networks. Consequently, chromatin regulators evolved to support this increased complexity. The ATP-dependent chromatin remodelers of the SWI/SNF family are multiprotein complexes that modulate nucleosome positioning and appear under different configurations, which perform distinct functions. While the composition, architecture, and activity of these subclasses are well understood in a limited number of fungal and animal model organisms, the lack of comprehensive information in other eukaryotic organisms precludes the identification of a reliable evolutionary model of SWI/SNF complexes. Here, we performed a systematic analysis using 36 species from animal, fungal, and plant lineages to assess the conservation of known SWI/SNF subunits across eukaryotes. We identified evolutionary relationships that allowed us to propose the composition of a hypothetical ancestral SWI/SNF complex in the last eukaryotic common ancestor. This last common ancestor appears to have undergone several rounds of lineage-specific subunit gains and losses, shaping the current conformation of the known subclasses in animals and fungi. In addition, our results unravel a plant SWI/SNF complex, reminiscent of the animal BAF subclass, which incorporates a set of plant-specific subunits of still unknown function.

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and 5’ transcript length determination in Arabidopsis

“…We recently identified an evolutionarily conserved plant SWI/SNF complex reminiscent of the mammalian BAF subclass (35). In the present study we report the function of the plant BAF-like complex, which regulates the position of the +1 nucleosome of thousands of genes and affects their 5’ transcript length.…”

“…Immunoprecipitation followed by mass spectrometry was done as previously described (35). Briefly, 8 g of inflorescences from one untransformed Col-0 replicate, two independent lines of TPF2-FLAG and two independent lines of MINU2-FLAG, were ground in liquid nitrogen and resuspended in 40 ml IP buffer (50 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl 2 , 10% glycerol, 0.1% NP40, 0.5 mM DTT, 1 mM PMSF, 1 μg/μL pepstatin, and 1× Complete EDTA-Free (Sigma).…”

“…However, there is a significant lack of information about the components and molecular function of the plant BAF-like complex. Through proteomics, we recently reported the composition of this complex in Arabidopsis, which incorporates conserved subunits as well as a set of plant-specific subunits of unknown function (35). Among them, we found two paralogs of an evolutionarily-conserved signature subunit –SMARCG-that we named TRIPLE PHD FINGERS (TPF1 and TFP2) and that have not been characterized in plants.…”

“…Functional characterization of the DPF/PHF10 proteins in mammals has demonstrated their important function in the complex through dynamic incorporation upon different cellular contexts and its role in the recruitment of the complex to the chromatin mediated by their tandem PHD histone reader domains (46,49,50). The TPF proteins present three tandem PHD domains as well as a C-terminal Tudor domain, also involved in histone reading, suggesting a possible functional conservation with their animal counterparts (35).…”

SMARCB1-Deficient Cancers: Novel Molecular Insights and Therapeutic Vulnerabilities

“…SMARCB1 is conserved in nearly all eukaryotic species [ 70 ]. The winged helix domain appears dispensable within the plant species, A. thaliana , while the other three domains, RPT1, RPT2, and CCD, have numerous conserved regions throughout ( Figure 2 ).…”