Clapier, C. R. Sophisticated conversations between chromatin and chromatin remodelers, and dissonances in cancer. Int. J. Mol. Sci. https://doi.org/10.3390/ijms22115578 (2021).
Kadoch, C. & Crabtree, G. R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics. Sci. Adv. 1, e1500447 (2015).
Jerzmanowski, A. SWI/SNF chromatin remodeling and linker histones in plants. Biochim. Biophys. Acta 1769, 330–345 (2007).
[+]
Clapier, C. R. Sophisticated conversations between chromatin and chromatin remodelers, and dissonances in cancer. Int. J. Mol. Sci. https://doi.org/10.3390/ijms22115578 (2021).
Kadoch, C. & Crabtree, G. R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics. Sci. Adv. 1, e1500447 (2015).
Jerzmanowski, A. SWI/SNF chromatin remodeling and linker histones in plants. Biochim. Biophys. Acta 1769, 330–345 (2007).
Dingwall, A. K. et al. The Drosophila snr1 and brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. Mol. Biol. Cell 6, 777–791 (1995).
Stern, M., Jensen, R. & Herskowitz, I. Five SWI genes are required for expression of the HO gene in yeast. J. Mol. Biol. 178, 853–868 (1984).
Sarnowska, E. et al. The role of SWI/SNF chromatin remodeling complexes in hormone crosstalk. Trends Plant Sci. 21, 594–608 (2016).
Ho, L. & Crabtree, G. R. Chromatin remodelling during development. Nature 463, 474–484 (2010).
Hodges, C., Kirkland, J. G. & Crabtree, G. R. The many roles of BAF (mSWI/SNF) and PBAF complexes in cancer. Cold Spring Harbor Perspect. Med. https://doi.org/10.1101/cshperspect.a026930 (2016).
Wang, W. et al. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J. 15, 5370–5382 (1996).
Kadoch, C. et al. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat. Genet. 45, 592–601 (2013).
Alpsoy, A. & Dykhuizen, E. C. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. J. Biol. Chem. 293, 3892–3903 (2018).
Wang, X. et al. BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat. Commun. 10, 1881 (2019).
Michel, B. C. et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat. Cell Biol. 20, 1410–1420 (2018).
Pan, J. et al. Interrogation of mammalian protein complex structure, function, and membership using genome-scale fitness screens. Cell Syst. 6, 555–568 (2018). e557.
Lessard, J. et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55, 201–215 (2007).
Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl Acad. Sci. USA 106, 5181–5186 (2009).
Staahl, B. T. et al. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. J. Neurosci. 33, 10348–10361 (2013).
Wilsker, D. et al. Nomenclature of the ARID family of DNA-binding proteins. Genomics 86, 242–251 (2005).
Nie, Z. et al. A specificity and targeting subunit of a human SWI/SNF family-related chromatin-remodeling complex. Mol. Cell. Biol. 20, 8879–8888 (2000).
Mohrmann, L. et al. Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol. Cell. Biol. 24, 3077–3088 (2004).
Satterwhite, E. et al. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood 98, 3413–3420 (2001).
Xue, Y. et al. The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. Proc. Natl Acad. Sci. USA 97, 13015–13020 (2000).
Cairns, B. R. et al. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4, 715–723 (1999).
Wang, W. et al. Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. Proc. Natl Acad. Sci. USA 95, 492–498 (1998).
Monahan, B. J. et al. Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Nat. Struct. Mol. Biol. 15, 873–880 (2008).
Papoulas, O. et al. The HMG-domain protein BAP111 is important for the function of the BRM chromatin-remodeling complex in vivo. Proc. Natl Acad. Sci. USA 98, 5728–5733 (2001).
Vercruyssen, L. et al. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 26, 210–229 (2014).
Jarończyk, K. et al. Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis. Plant Commun. 2, 100174 (2021).
Yu, Y. et al. Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis. Mol. Plant 14, 888–904 (2021).
Nelissen, H. et al. Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf. Plant Cell 27, 1605–1619 (2015).
Yu, Y. et al. BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes. Nat. Plants 6, 996–1007 (2020).
Kim, J. H. & Tsukaya, H. Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. J. Exp. Bot. 66, 6093–6107 (2015).
Wilson, B., Erdjument-Bromage, H., Tempst, P. & Cairns, B. R. The RSC chromatin remodeling complex bears an essential fungal-specific protein module with broad functional roles. Genetics 172, 795–809 (2006).
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
Lu, R. & Wang, G. G. Tudor: a versatile family of histone methylation ‘readers’. Trends Biochem. Sci. 38, 546–555 (2013).
Buszewicz, D. et al. HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. Plant Cell Environ. 39, 2108–2122 (2016).
Zhang, H. et al. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc. Natl Acad. Sci. USA 110, 8290–8295 (2013).
Pandey, R. et al. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30, 5036–5055 (2002).
Marcum, R. D., Reyes, A. A. & He, Y. Structural insights into the evolutionarily conserved BAF chromatin remodeling complex. Biology https://doi.org/10.3390/biology9070146 (2020).
Mani, U., Goutham, R. N. A. & Mohan, S. S. SWI/SNF infobase-an exclusive information portal for SWI/SNF remodeling complex subunits. PLoS ONE 12, e0184445 (2017).
He, S. et al. Structure of nucleosome-bound human BAF complex. Science 367, 875–881 (2020).
Mashtalir, N. et al. A structural model of the endogenous human BAF complex informs disease mechanisms. Cell 183, 802–817 (2020). e824.
Wang, C. et al. Structure of the yeast Swi/Snf complex in a nucleosome free state. Nat. Commun. 11, 3398 (2020).
Han, Y., Reyes, A. A., Malik, S. & He, Y. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature 579, 452–455 (2020).
Ye, Y. et al. Structure of the RSC complex bound to the nucleosome. Science 366, 838–843 (2019).
Sang, Y. et al. Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects. Plant J. 72, 1000–1014 (2012).
Law, J. A. et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498, 385–389 (2013).
Clayton, C. Regulation of gene expression in trypanosomatids: living with polycistronic transcription. Open Biol. 9, 190072 (2019).
Wallace, I. M., O’Sullivan, O., Higgins, D. G. & Notredame, C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34, 1692–1699 (2006).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Wongpalee, S. P. et al. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nat. Commun. 10, 3916 (2019).
Jami-Alahmadi, Y., Pandey, V., Mayank, A. K. & Wohlschlegel, J. A. A robust method for packing high resolution C18 RP-nano-HPLC columns. J. Vis. Exp. https://doi.org/10.3791/62380 (2021).
Izquierdo-González, J. J. et al. Proteomic analysis of goat milk kefir: profiling the fermentation-time dependent protein digestion and identification of potential peptides with biological activity. Food Chem. 295, 456–465 (2019).
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
Curtis, M. D. & Grossniklaus, U. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462–469 (2003).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Pettersen, E. F. et al. UCSF chimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
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