Mechanism of action of the SWI/SNF family complexes

References

• Luger K, Mäder AW, Richmond RK, et al. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 1997;389(6648):251–14.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem. 2009;78(1):273–304.
   PubMedGoogle Scholar
• Egel R, Beach DH, Klar AJ. Genes required for initiation and resolution steps of mating-type switching in fission yeast. Proc Natl Acad Sci U S A. 1984;81(11):3481–3485.
   PubMed Web of Science ®Google Scholar
• Neigeborn L, Carlson M. GENES AFFECTING THE REGULATION OF SUC2 GENE EXPRESSION BY GLUCOSE REPRESSION IN SACCHAROMYCES CEREVISIAE. Genetics. 1984;108(4):845–858.
   PubMed Web of Science ®Google Scholar
• Sudarsanam P, Iyer VR, Brown PO, et al. Whole-genome expressionanalysis of snf/swi mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2000;97(7):3364–3369.
   PubMed Web of Science ®Google Scholar
• Hartley PD, Madhani HD. Mechanisms that specify promoter nucleosome location and identity. Cell. 2009;137(3):445–458.
   PubMed Web of Science ®Google Scholar
• Kasten MM, Clapier CR, Cairns BR. SnapShot: chromatin remodeling: SWI/SNF. Cell. 2011;144(2):310 e311.
   Web of Science ®Google Scholar
• Michel BC, D’Avino AR, Cassel SH, et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat Cell Biol. 2018;20(12):1410–1420.
   PubMed Web of Science ®Google Scholar
• Alpsoy A, Dykhuizen EC. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. J Biol Chem. 2018;293(11):3892–3903.
   PubMed Web of Science ®Google Scholar
• Sokpor G, Xie Y, Rosenbusch J, et al. Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders. Front Mol Neurosci. 2017;10:243.
   PubMed Web of Science ®Google Scholar
• Hodges C, Kirkland JG, Crabtree GR. The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harb Perspect Med. 2016;6(8):a026930.
   PubMed Web of Science ®Google Scholar
• Mittal P, Roberts CWM. The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol. 2020;17(7):435–448.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Kasten MM, Parnell TJ, et al. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Mol Cell. 2016;62(3):453–461.
   PubMed Web of Science ®Google Scholar
• Cairns BR, Levinson RS, Yamamoto KR, et al. Essential role of Swp73p in the function of yeast Swi/Snf complex. Genes Dev. 1996;10(17):2131–2144.
   PubMed Web of Science ®Google Scholar
• Angus-Hill ML, Schlichter A, Roberts D, et al. A Rsc3/Rsc30 Zinc Cluster Dimer Reveals Novel Roles for the Chromatin Remodeler RSC in Gene Expression and Cell Cycle Control. Mol Cell. 2001;7(4):741–751.
   PubMed Web of Science ®Google Scholar
• Badis G, Chan ET, van Bakel H, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell. 2008;32(6):878–887.
   PubMed Web of Science ®Google Scholar
• Han Y, Reyes AA, Malik S, et al. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature. 2020;579(7799):452–455.
   PubMed Web of Science ®Google Scholar
• He Z, Chen K, Ye Y, et al. Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. Cell Discov. 2021;7(1):28.
   PubMed Web of Science ®Google Scholar
• Wang C, Guo Z, Zhan X, et al. Structure of the yeast Swi/Snf complex in a nucleosome free state. Nat Commun. 2020;11(1):3398.
   PubMed Web of Science ®Google Scholar
• Ye Y, Wu H, Chen K, et al. Structure of the RSC complex bound to the nucleosome. Science. 2019;366(6467):838–843.
   PubMed Web of Science ®Google Scholar
• Wagner FR, Dienemann C, Wang H, et al. Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Nature. 2020;579(7799):448–451.
   PubMed Web of Science ®Google Scholar
• Patel AB, Moore CM, Greber BJ, et al. Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. Elife. 2019;8:e54449.
   PubMed Web of Science ®Google Scholar
• He S, Wu Z, Tian Y, et al. Structure of nucleosome-bound human BAF complex. Science. 2020;367(6480):875–881.
   PubMed Web of Science ®Google Scholar
• Mashtalir N, Suzuki H, Farrell DP, et al. A structural model of the endogenous human BAF complex informs disease mechanisms. Cell. 2020;183(3):802–817.e824.
   PubMed Web of Science ®Google Scholar
• Yuan J, Chen K, Zhang W, et al. Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature. 2022;605(7908):166–171.
   PubMed Web of Science ®Google Scholar
• Wang L, Yu J, Yu Z, et al. Structure of nucleosome-bound human PBAF complex. BioRxiv, 2022. Accessed20 May 2022. https://doi.org/10.1101/2022.05.20.492795
   Google Scholar
• Asturias FJ, Chung WH, Kornberg RD, et al. Structural analysis of the RSC chromatin-remodeling complex. Proc Natl Acad Sci U S A. 2002;99(21):13477–13480.
   PubMed Web of Science ®Google Scholar
• Smith CL, Horowitz-Scherer R, Flanagan JF, et al. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat Struct Biol. 2003;10(2):141–145.
   PubMedGoogle Scholar
• Leschziner AE, Lemon B, Tjian R, et al. Structural studies of the human PBAF chromatin-remodeling complex. Structure. 2005;13(2):267–275.
   PubMed Web of Science ®Google Scholar
• Leschziner AE, Saha A, Wittmeyer J, et al. Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A. 2007;104(12):4913–4918.
   PubMed Web of Science ®Google Scholar
• Chaban Y, Ezeokonkwo C, Chung W-H, et al. Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol. 2008;15(12):1272–1277.
   PubMed Web of Science ®Google Scholar
• Dechassa ML, Zhang B, Horowitz-Scherer R, et al. Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol. 2008;28(19):6010–6021.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Wang X, Xin J, et al. Architecture of SWI/SNF chromatin remodeling complex. Protein Cell. 2018;9(12):1045–1049.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Iwasa J, Cairns BR, et al. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol. 2017;18(7):407–422.
   PubMed Web of Science ®Google Scholar
• Yan L, Chen Z. A Unifying Mechanism of DNA Translocation Underlying Chromatin Remodeling. Trends Biochem Sci. 2020;45(3):217–227.
   PubMed Web of Science ®Google Scholar
• Liu X, Li M, Xia X, et al. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature. 2017;544(7651):440–445.
   PubMed Web of Science ®Google Scholar
• Sen P, Ghosh S, Pugh BF, et al. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Res. 2011;39(21):9155–9166.
   PubMed Web of Science ®Google Scholar
• Sen P, Vivas P, Dechassa ML, et al. The SnAC domain of SWI/SNF is a histone anchor required for remodeling. Mol Cell Biol. 2013;33(2):360–370.
   PubMed Web of Science ®Google Scholar
• McGinty RK, Tan S. Principles of nucleosome recognition by chromatin factors and enzymes. Curr Opin Struct Biol. 2021;71:16–26.
   PubMed Web of Science ®Google Scholar
• Baker RW, Reimer JM, Carman PJ, et al. Structural insights into assembly and function of the RSC chromatin remodeling complex. Nat Struct Mol Biol. 2021;28(1):71–80.
   PubMed Web of Science ®Google Scholar
• Schubert HL, Wittmeyer J, Kasten MM, et al. Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A. 2013;110(9):3345–3350.
   PubMed Web of Science ®Google Scholar
• Cairns BR, Erdjument-Bromage H, Tempst P, et al. Two Actin-Related Proteins Are Shared Functional Components of the Chromatin-Remodeling Complexes RSC and SWI/SNF. Mol Cell. 1998;2(5):639–651.
   PubMed Web of Science ®Google Scholar
• Szerlong H, Hinata K, Viswanathan R, et al. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol. 2008;15(5):469–476.
   PubMed Web of Science ®Google Scholar
• Xia X, Liu X, Li T, et al. Structure of chromatin remodeler Swi2/Snf2 in the resting state. Nat Struct Mol Biol. 2016;23(8):722–729.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Verma N, Parnell TJ, et al. Cancer-Associated Gain-of-Function Mutations Activate a SWI/SNF-Family Regulatory Hub. Mol Cell. 2020;80(4):712–725 e715.
   PubMed Web of Science ®Google Scholar
• Valencia AM, Collings CK, Dao HT, et al. Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling. Cell. 2019;179(6):1342–1356 e1323.
   PubMed Web of Science ®Google Scholar
• Mashtalir N, Dao HT, Sankar A, et al. Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes. Science. 2021;373(6552):306–315.
   PubMed Web of Science ®Google Scholar
• Dann GP, Liszczak GP, Bagert JD, et al. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature. 2017;548(7669):607–611.
   PubMed Web of Science ®Google Scholar
• Cakiroglu A, Clapier CR, Ehrensberger AH, et al. Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes. Genome Res. 2019;29(6):988–998.
   PubMed Web of Science ®Google Scholar
• Lemon B, Inouye C, King DS, et al. Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature. 2001;414(6866):924–928.
   PubMed Web of Science ®Google Scholar
• Pan D, Kobayashi A, Jiang P, et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science. 2018;359:770–775.
   PubMed Web of Science ®Google Scholar
• Reichen C, Hansen S, Pluckthun A. Modular peptide binding: from a comparison of natural binders to designed armadillo repeat proteins. J Struct Biol. 2014;185(2):147–162.
   PubMed Web of Science ®Google Scholar
• Nie Z, Xue Y, Yang D, et al. A specificity and targeting subunit of a human SWI/SNF family-related chromatin-remodeling complex. Mol Cell Biol. 2000;20(23):8879–8888.
   PubMed Web of Science ®Google Scholar
• Hsiao PW, Fryer CJ, Trotter KW, et al. BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. Mol Cell Biol. 2003;23(17):6210–6220.
   PubMed Web of Science ®Google Scholar
• Priam P, Krasteva V, Rousseau P, et al. SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. Nat Genet. 2017;49(5):753–764.
   PubMed Web of Science ®Google Scholar
• Witzel M, Petersheim D, Fan Y, et al. Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat Genet. 2017;49(5):742–752.
   PubMed Web of Science ®Google Scholar
• Jiang H, Cao H-J, Ma N, et al. Chromatin remodeling factor ARID2 suppresses hepatocellular carcinoma metastasis via DNMT1-Snail axis. Proc Natl Acad Sci U S A. 2020;117(9):4770–4780.
   PubMed Web of Science ®Google Scholar
• Allen MD, Freund SMV, Bycroft M, et al. SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site. Commun Biol. 2021;4(1):528.
   PubMed Web of Science ®Google Scholar
• Wang W, Chi T, Xue Y, et al. Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. Proceedings of the National Academy of Sciences 95, 492–498 (1998). https://doi.org/10.1073/pnas.95.2.492 Accessed20 January 1998
   Google Scholar
• Smith MJ, O’Sullivan J, Bhaskar SS, et al. Loss-of-function mutations in SMARCE1 cause an inherited disorder of multiple spinal meningiomas. Nat Genet. 2013;45(3):295–298.
   PubMed Web of Science ®Google Scholar
• St Pierre R, Collings CK, Samé Guerra DD, et al. SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma. Nat Genet. 2022;54(6):861–873.
   PubMed Web of Science ®Google Scholar
• Wang X, Wang S, Troisi EC, et al. BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat Commun. 2019;10(1):1881.
   PubMed Web of Science ®Google Scholar
• Brien GL, Remillard D, Shi J, et al. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. Elife. 2018;7:e41305.
   PubMed Web of Science ®Google Scholar
• Wei Z, Yoshihara E, He N, et al. Vitamin D Switches BAF Complexes to Protect beta Cells. Cell. 2018;173(5):1135–1149 e1115.
   PubMed Web of Science ®Google Scholar
• Levine DA, Mueller JJ, Levine DA, et al. Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. Gynecol Oncol. 2014;134(2):439–440.
   Web of Science ®Google Scholar
• Ramos P, Karnezis AN, Craig DW, et al. Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nat Genet. 2014;46(5):427–429.
   PubMed Web of Science ®Google Scholar
• Buscarlet M, Krasteva V, Ho L, et al. Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. Blood. 2014;123(11):1720–1728.
   PubMed Web of Science ®Google Scholar
• Lin H, Wong RP, Martinka M, et al. BRG1 expression is increased in human cutaneous melanoma. Br J Dermatol. 2010;163(3):502–510.
   PubMed Web of Science ®Google Scholar
• Saladi SV, Keenen B, Marathe HG, et al. Modulation of extracellular matrix/adhesion molecule expression by BRG1 is associated with increased melanoma invasiveness. Mol Cancer. 2010;9(1):280.
   PubMedGoogle Scholar
• Ehrenhöfer-Wölfer K, Puchner T, Schwarz C, et al. SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines. Sci Rep. 2019;9(1):11661.
   PubMedGoogle Scholar
• Wilson BG, Wang X, Shen X, et al. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell. 2010;18(4):316–328.
   PubMed Web of Science ®Google Scholar
• Wang X, Lee RS, Alver BH, et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017;49(2):289–295.
   PubMed Web of Science ®Google Scholar
• Nakayama RT, Pulice JL, Valencia AM, et al. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017;49(11):1613–1623.
   PubMed Web of Science ®Google Scholar
• Dykhuizen EC, Hargreaves DC, Miller EL, et al. BAF complexes facilitate decatenation of DNA by topoisomerase IIalpha. Nature. 2013;497(7451):624–627.
   PubMed Web of Science ®Google Scholar
• Fernando TM, Piskol R, Bainer R, et al. Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients. Nat Commun. 2020;11(1):5551.
   PubMed Web of Science ®Google Scholar
• Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269):l1.
   Web of Science ®Google Scholar
• Mashtalir N, D’Avino AR, Michel BC, et al. Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell. 2018;175(5):1272–1288 e1220.
   PubMed Web of Science ®Google Scholar
• Varela I, Tarpey P, Raine K, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature. 2011;469(7331):539–542.
   PubMed Web of Science ®Google Scholar
• Gao W, Li W, Xiao T, et al. Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL −/− clear cell renal carcinoma. Proc Natl Acad Sci U S A. 2017;114(5):1027–1032.
   PubMed Web of Science ®Google Scholar
• Espana-Agusti J, Warren A, Chew SK, et al. Loss of PBRM1 rescues VHL dependent replication stress to promote renal carcinogenesis. Nat Commun. 2017;8:2026.
   PubMed Web of Science ®Google Scholar
• Nargund AM, Pham CG, Dong Y, et al. The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Cell Rep. 2017;18:2893–2906.
   PubMed Web of Science ®Google Scholar
• Staahl BT, Tang J, Wu W, et al. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. J Neurosci. 2013;33(25):10348–10361.
   PubMed Web of Science ®Google Scholar
• Sousa SB, Hennekam RC, Nicolaides-Baraitser Syndrome International C. Phenotype and genotype in Nicolaides-Baraitser syndrome. Am J Med Genet C Semin Med Genet. 2014;166C(3):302–314.
   PubMedGoogle Scholar
• Santen GW, Aten E, Vulto-van Silfhout AT, et al. Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients. Hum Mutat. 2013;34(11):1519–1528.
   PubMed Web of Science ®Google Scholar
• Wieczorek D, Bogershausen N, Beleggia F, et al. A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling. Hum Mol Genet. 2013;22(25):5121–5135.
   PubMed Web of Science ®Google Scholar
• Xiao L, Parolia A, Qiao Y, et al. Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer. Nature. 2022;601(7893):434–439.
   PubMed Web of Science ®Google Scholar
• Xu Y, Yan W, Chen X. SNF5, a core component of the SWI/SNF complex, is necessary for p53 expression and cell survival, in part through eIF4E. Oncogene. 2010;29(28):4090–4100.
   PubMed Web of Science ®Google Scholar
• Kazantseva A, Sepp M, Kazantseva J, et al. N-terminally truncated BAF57 isoforms contribute to the diversity of SWI/SNF complexes in neurons. J Neurochem. 2009;109(3):807–818.
   PubMed Web of Science ®Google Scholar
• Selvanathan SP, Graham GT, Grego AR, et al. EWS-FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex. Nucleic Acids Res. 2019;47(18):9619–9636.
   PubMed Web of Science ®Google Scholar