The Role and Activity of SWI/SNF Chromatin Remodelers

Abstract

SWITCH deficient SUCROSE NONFERMENTING (SWI/SNF) class chromatin remodeling complexes (CRCs) use the energy derived from ATP hydrolysis to facilitate access of proteins to the genomic DNA for transcription, replication, and DNA repair. Uniquely, SWI/SNF CRCs can both slide the histone octamer along the DNA or eject it from the DNA. Given their ability to change the chromatin status quo, SWI/SNF remodelers are critical for cell fate reprogramming with pioneer and other transcription factors, for responses to environmental challenges, and for disease prevention. Recent cryo-electron microscopy and mass spectrometry approaches have uncovered different subtypes of SWI/SNF complexes with unique properties and functions. At the same time, tethering or rapid depletion and inactivation of SWI/SNF have provided novel insight into SWI/SNF requirements for enhancer activity and into balancing chromatin compaction and accessibility in concert with Polycomb complexes. Given their importance, SWI/SNF recruitment to genomic locations by transcription factors and their biochemical activity is tightly controlled. This review focuses on recent advances in our understanding of SWI/SNF CRCs in animals and plants and discusses the multiple nuclear and biological roles of SWI/SNF CRCs and how SWI/SNF activity is altered by complex subunit composition, posttranslational modifications, and the chromatin context to support proper development and response to extrinsic cues. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported byIn VivoCharacterizations and AI FacilitatedIn SilicoMechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis

“…7A-B). Binding of ARPs to the HSA domain of many nucleosome remodelers, as well as the adjunctive fashion in which such ARP and actin monomers interact with each other in the complexes, has been readily documented in yeast and mammals alike (Reyes et al, 2021; Bieluszewski et al, 2023). Additionally, many of these ARPs such as ACTL6A/B (Karlsson et al, 2021), as well as nucleosome remodelers such as SRCAP complex members (Karlsson et al, 2021; Sun et al, 2022), SMARCA family members (Chong et al, 2007; Farshad Niri et al 2021), INO80 (Serber et al, 2016), and EP400 (Karlsson et al, 2021), have been documented to be present across many developmental stages of the male germline.…”

“…In contrast, SWI/SNF complexes do not require an association with a RuvB hexamer and are implicated in transcriptional repression and upregulation through ZEB1 and CREST-dependent pathways (Sánchez-Tilló et al, 2010; Qiu & Ghosh, 2008) as well as have been characterized to be crucial components for the differentiation and development of cellular lineages (Paula Coutinho Toto et al, 2016; Alver et al, 2017; Smith et al, 2022). SWI/SNF complexes are known to contain Arp4, Arp6, Arp7, Arp8, Arp9, and actin in yeast while the mammalian equivalent BAF complexes contain ACTL6A, ACTL6B, and β-actin (Bieluszewski et al, 2023). Thus, we speculate that testis-specific ARP subunit swapping in chromatin remodelers may lead to germline-specific modification of processes such as affinity based associations, recruitment of epigenetic regulators, association with specific histone variants, nucleosome PTM recognition, and/or direct DNA binding.…”

Single‐cell transcriptomic analysis of pea shoot development and cell‐type‐specific responses to boron deficiency

“…SWI2A and SWI3C proteins are components of the SWITCH DEFECTIVE/SUCROSE NON‐FERMENTABLE (SWI/SNF) chromatin remodeling complex. The SWI/SNF complex regulates gene expression by altering chromatin structure (Bieluszewski et al., 2023). In SAM, these two TF genes not only respond to B deficiency signals but also play a central regulatory role by interacting with other TFs.…”

“…Members of the SWI/SNF complex, SWI3A and SWI3C , significantly responded to B deficiency in SAM and potentially act as core genes in the TF network, coordinating other TFs to regulate downstream signals. The SWI/SNF chromatin remodeling complex alters the contact between DNA and nucleosomes by utilizing ATP to make chromatin structures looser or tighter, thus affecting the accessibility of TFs and other regulatory proteins to specific genes (Bieluszewski et al., 2023). WUS expression in the OC region is activated by the SWI/SNF‐type ATPase SYD (Shen & Xu, 2009).…”

The SAS Chromatin-Remodeling Complex Mediates Inflorescence-Specific Chromatin Accessibility for Transcription Factor Binding

“…Previous studies have demonstrated that transcription factors either recruit SWI/SNF complexes to specific target genes or collaborate with SWI/SNF to regulate chromatin accessibility and transcriptional activation (Bieluszewski et al, 2023). In order to investigate how SAS-dependent chromatin accessibility is regulated during flower development, we examined whether the inflorescence-specific SAS-binding regions are enriched with any transcription factor-binding DNA motifs.…”