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ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery

Abstract

The AT-rich interaction domain (ARID) family of DNA-binding proteins is a group of transcription factors and chromatin regulators with a highly conserved ARID domain that recognizes specific AT-rich DNA sequences. Dysfunction of ARID family members has been implicated in various human diseases including cancers and intellectual disability. Among them, ARID3a has gained increasing attention due to its potential involvement in autoimmunity. In this article we provide an overview of the ARID family, focusing on the structure and biological functions of ARID3a. It explores the role of ARID3a in autoreactive B cells and its contribution to autoimmune diseases such as systemic lupus erythematosus and primary biliary cholangitis. Furthermore, we also discuss the potential for drug discovery targeting ARID3a and present a plan for future research in this field.

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Fig. 1: The human ARID family, which is classified into seven subfamilies, ARID1-5 and JARID1-2, based on the sequence homology of the shared ARID domain.
Fig. 2: Sequence alignment of the ARID domain of ARID proteins with known structures.
Fig. 3: ARID-DNA complexes.
Fig. 4: ARID3a plays a role in gene regulation.
Fig. 5: ARID3a and autoreactive B cells.
Fig. 6: ARID3a and SLE.

References

  1. Patsialou A, Wilsker D, Moran E. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 2005;33:66–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Zheng J, Wang Y, Hu J. Study of the shared gene signatures of polyarticular juvenile idiopathic arthritis and autoimmune uveitis. Front Immunol. 2023;14:1048598.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Sinha S, Chatterjee SS, Biswas M, Nag A, Banerjee D, De R, et al. SWI/SNF subunit expression heterogeneity in human aplastic anemia stem/progenitors. Exp Hematol. 2018;62:39–44.e2.

    Article  CAS  PubMed  Google Scholar 

  4. Ward JM, Rose K, Montgomery C, Adrianto I, James JA, Merrill JT, et al. Disease activity in systemic lupus erythematosus correlates with expression of the transcription factor AT-rich-interactive domain 3A. Arthritis Rheumatol. 2014;66:3404–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Li Y, Li Z, Chen R, Lian M, Wang H, Wei Y, et al. A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression. Nat Commun. 2023;14:1732.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Liu C, Yan S, Chen H, Wu Z, Li L, Li Y. Several genetic variants associated with systemic sclerosis in a Chinese Han population. Clin Rheumatol. 2023;42:773–81.

  7. Nyati KK, Zaman MM, Sharma P, Kishimoto T. Arid5a, an RNA-binding protein in immune regulation: RNA stability, inflammation, and autoimmunity. Trends Immunol. 2020;41:255–68.

    Article  CAS  PubMed  Google Scholar 

  8. Okada Y, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, et al. Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. Nat Genet. 2012;44:511–6.

    Article  CAS  PubMed  Google Scholar 

  9. Yang W, Tang H, Zhang Y, Tang X, Zhang J, Sun L, et al. Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. Am J Hum Genet. 2013;92:41–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tomer Y, Hasham A, Davies TF, Stefan M, Concepcion E, Keddache M, et al. Fine mapping of loci linked to autoimmune thyroid disease identifies novel susceptibility genes. J Clin Endocrinol Metab. 2013;98:E144–52.

    Article  CAS  PubMed  Google Scholar 

  11. Zhao M, Liang G, Wu X, Wang S, Zhang P, Su Y, et al. Abnormal epigenetic modifications in peripheral blood mononuclear cells from patients with alopecia areata. Br J Dermatol. 2012;166:226–73.

    Article  CAS  PubMed  Google Scholar 

  12. Umair M, Fazazi MR, Rangachari M. Biological sex as a critical variable in CD4(+) effector T cell function in preclinical models of multiple sclerosis. Antioxid Redox Signal. 2022;37:135–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Doss P, Umair M, Baillargeon J, Fazazi R, Fudge N, Akbar I, et al. Male sex chromosomal complement exacerbates the pathogenicity of Th17 cells in a chronic model of central nervous system autoimmunity. Cell Rep. 2021;34:108833.

    Article  CAS  PubMed  Google Scholar 

  14. Pereira RM, Martinez GJ, Engel I, Cruz-Guilloty F, Barboza BA, Tsagaratou A, et al. Jarid2 is induced by TCR signalling and controls iNKT cell maturation. Nat Commun. 2014;5:4540.

    Article  CAS  PubMed  Google Scholar 

  15. Zheng Y, Ge W, Ma Y, Xie G, Wang W, Han L, et al. miR-155 regulates IL-10-producing CD24(hi)CD27(+) B cells and impairs their function in patients with Crohn’s disease. Front Immunol. 2017;8:914.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Xu HE, Lambert MH, Montana VG, Plunket KD, Moore LB, Collins JL, et al. Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors. Proc Natl Acad Sci USA. 2001;98:13919–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Xu HE, Stanley TB, Montana VG, Lambert MH, Shearer BG, Cobb JE, et al. Structural basis for antagonist-mediated recruitment of nuclear co-repressors by PPARalpha. Nature. 2002;415:813–7.

    Article  CAS  PubMed  Google Scholar 

  18. Kim D, Probst L, Das C, Tucker PW. REKLES is an ARID3-restricted multifunctional domain. J Biol Chem. 2007;282:15768–77.

    Article  CAS  PubMed  Google Scholar 

  19. Ren J, Yao H, Hu W, Perrett S, Gong W, Feng Y. Structural basis for the DNA-binding activity of human ARID4B Tudor domain. J Biol Chem. 2021;296:100506.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006;439:811–6.

    Article  CAS  PubMed  Google Scholar 

  21. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem. 2022;403:731–47.

    Article  CAS  PubMed  Google Scholar 

  23. Whitson RH, Huang T, Itakura K. The novel Mrf-2 DNA-binding domain recognizes a five-base core sequence through major and minor-groove contacts. Biochem Biophys Res Commun. 1999;258:326–31.

    Article  CAS  PubMed  Google Scholar 

  24. Valentine SA, Chen G, Shandala T, Fernandez J, Mische S, Saint R, et al. Dorsal-mediated repression requires the formation of a multiprotein repression complex at the ventral silencer. Mol Cell Biol. 1998;18:6584–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Gregory SL, Kortschak RD, Kalionis B, Saint R. Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins. Mol Cell Biol. 1996;16:792–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW. The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev. 1995;9:3067–82.

    Article  CAS  PubMed  Google Scholar 

  27. Iwahara J, Clubb RT. Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID). EMBO J. 1999;18:6084–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev. 2005;29:231–62.

    Article  CAS  PubMed  Google Scholar 

  29. Giri M, Maulik A, Singh M. Signatures of specific DNA binding by the AT-Rich interaction domain of BAF250a. Biochemistry. 2020;59:100–13.

    Article  CAS  PubMed  Google Scholar 

  30. Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT. The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J. 2002;21:1197–209.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Maulik A, Giri M, Singh M. Molecular determinants of complex formation between DNA and the AT-rich interaction domain of BAF250a. FEBS Lett. 2019;593:2716–29.

    Article  CAS  PubMed  Google Scholar 

  32. Giri M, Gupta P, Maulik A, Gracias M, Singh M. Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b. Protein Sci. 2022;31:e4294.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W, Mach B, et al. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature. 2000;403:916–21.

    Article  CAS  PubMed  Google Scholar 

  34. Gajiwala KS, Burley SK. Winged helix proteins. Curr Opin Struct Biol. 2000;10:110–6.

    Article  CAS  PubMed  Google Scholar 

  35. Kortschak RD, Tucker PW, Saint R. ARID proteins come in from the desert. Trends Biochem Sci. 2000;25:294–9.

    Article  CAS  PubMed  Google Scholar 

  36. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, et al. BioMagResBank. Nucleic Acids Res. 2008;36:D402–8.

    Article  CAS  PubMed  Google Scholar 

  37. van Zundert GCP, Rodrigues J, Trellet M, Schmitz C, Kastritis PL, Karaca E, et al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol. 2016;428:720–5.

    Article  PubMed  Google Scholar 

  38. Murphy FVT, Churchill ME. Nonsequence-specific DNA recognition: a structural perspective. Structure. 2000;8:R83–9.

    Article  CAS  PubMed  Google Scholar 

  39. Yuan J, Chen K, Zhang W, Chen Z. Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature. 2022;605:166–71.

    Article  CAS  PubMed  Google Scholar 

  40. Saadat K, Lestari W, Pratama E, Ma T, Iseki S, Tatsumi M, et al. Distinct and overlapping roles of ARID3A and ARID3B in regulating E2F‑dependent transcription via direct binding to E2F target genes. Int J Oncol. 2021;58:12.

  41. Shaham S, Bargmann CI. Control of neuronal subtype identity by the C. elegans ARID protein CFI-1. Genes Dev. 2002;16:972–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kaplan MH, Zong RT, Herrscher RF, Scheuermann RH, Tucker PW. Transcriptional activation by a matrix associating region-binding protein. Contextual requirements for the function of bright. J Biol Chem. 2001;276:21325–30.

    Article  CAS  PubMed  Google Scholar 

  43. Goebel P, Montalbano A, Ayers N, Kompfner E, Dickinson L, Webb CF, et al. High frequency of matrix attachment regions and cut-like protein x/CCAAT-displacement protein and B cell regulator of IgH transcription binding sites flanking Ig V region genes. J Immunol. 2002;169:2477–87.

    Article  CAS  PubMed  Google Scholar 

  44. Wilsker D, Probst L, Wain HM, Maltais L, Tucker PW, Moran E. Nomenclature of the ARID family of DNA-binding proteins. Genomics. 2005;86:242–51.

    Article  CAS  PubMed  Google Scholar 

  45. Liu G, Huang YJ, Xiao R, Wang D, Acton TB, Montelione GT. Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: a human cancer protein interaction network target. Proteins. 2010;78:2170–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Invernizzi G, Tiberti M, Lambrughi M, Lindorff-Larsen K, Papaleo E. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops. PLoS Comput Biol. 2014;10:e1003744.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Vishveshwara S, Ghosh A, Hansia P. Intra and inter-molecular communications through protein structure network. Curr Protein Pept Sci. 2009;10:146–60.

    Article  CAS  PubMed  Google Scholar 

  48. Böde C, Kovács IA, Szalay MS, Palotai R, Korcsmáros T, Csermely P. Network analysis of protein dynamics. FEBS Lett. 2007;581:2776–82.

    Article  PubMed  Google Scholar 

  49. Rajaiya J, Nixon JC, Ayers N, Desgranges ZP, Roy AL, Webb CF. Induction of immunoglobulin heavy-chain transcription through the transcription factor Bright requires TFII-I. Mol Cell Biol. 2006;26:4758–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Nixon JC, Rajaiya J, Webb CF. Mutations in the DNA-binding domain of the transcription factor Bright act as dominant negative proteins and interfere with immunoglobulin transactivation. J Biol Chem. 2004;279:52465–72.

    Article  CAS  PubMed  Google Scholar 

  51. Webb C, Zong RT, Lin D, Wang Z, Kaplan M, Paulin Y, et al. Differential regulation of immunoglobulin gene transcription via nuclear matrix-associated regions. Cold Spring Harb Symp Quant Biol. 1999;64:109–18.

    Article  CAS  PubMed  Google Scholar 

  52. Tu S, Teng YC, Yuan C, Wu YT, Chan MY, Cheng AN, et al. The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. Nat Struct Mol Biol. 2008;15:419–21.

    Article  CAS  PubMed  Google Scholar 

  53. Scibetta AG, Santangelo S, Coleman J, Hall D, Chaplin T, Copier J, et al. Functional analysis of the transcription repressor PLU-1/JARID1B. Mol Cell Biol. 2007;27:7220–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Kim S, Zhang Z, Upchurch S, Isern N, Chen Y. Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition. J Biol Chem. 2004;279:16670–6.

    Article  CAS  PubMed  Google Scholar 

  55. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42:D764–70.

    Article  CAS  PubMed  Google Scholar 

  56. Rajaiya J, Hatfield M, Nixon JC, Rawlings DJ, Webb CF. Bruton’s tyrosine kinase regulates immunoglobulin promoter activation in association with the transcription factor Bright. Mol Cell Biol. 2005;25:2073–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Webb CF, Das C, Eneff KL, Tucker PW. Identification of a matrix-associated region 5’ of an immunoglobulin heavy chain variable region gene. Mol Cell Biol. 1991;11:5206–11.

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Lin D, Ippolito GC, Zong RT, Bryant J, Koslovsky J, Tucker P. Bright/ARID3A contributes to chromatin accessibility of the immunoglobulin heavy chain enhancer. Mol Cancer. 2007;6:23.

    Article  PubMed  PubMed Central  Google Scholar 

  59. Cockerill PN, Yuen MH, Garrard WT. The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem. 1987;262:5394–7.

    Article  CAS  PubMed  Google Scholar 

  60. Bode J, Benham C, Knopp A, Mielke C. Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements). Crit Rev Eukaryot Gene Expr. 2000;10:73–90.

    Article  CAS  PubMed  Google Scholar 

  61. Scheuermann RH, Garrard WT. MARs of antigen receptor and co-receptor genes. Crit Rev Eukaryot Gene Expr. 1999;9:295–310.

    Article  CAS  PubMed  Google Scholar 

  62. Nixon JC, Ferrell S, Miner C, Oldham AL, Hochgeschwender U, Webb CF. Transgenic mice expressing dominant-negative bright exhibit defects in B1 B cells. J Immunol. 2008;181:6913–22.

    Article  CAS  PubMed  Google Scholar 

  63. Kim D, Tucker PW. A regulated nucleocytoplasmic shuttle contributes to Bright’s function as a transcriptional activator of immunoglobulin genes. Mol Cell Biol. 2006;26:2187–201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sacristán C, Tussié-Luna MI, Logan SM, Roy AL. Mechanism of Bruton’s tyrosine kinase-mediated recruitment and regulation of TFII-I. J Biol Chem. 2004;279:7147–58.

    Article  PubMed  Google Scholar 

  65. Webb CF, Yamashita Y, Ayers N, Evetts S, Paulin Y, Conley ME, et al. The transcription factor Bright associates with Bruton’s tyrosine kinase, the defective protein in immunodeficiency disease. J Immunol. 2000;165:6956–65.

    Article  CAS  PubMed  Google Scholar 

  66. Liao TT, Hsu WH, Ho CH, Hwang WL, Lan HY, Lo T, et al. let-7 modulates chromatin configuration and target gene repression through regulation of the ARID3B complex. Cell Rep. 2016;14:520–33.

    Article  CAS  PubMed  Google Scholar 

  67. Rhee C, Lee BK, Beck S, Anjum A, Cook KR, Popowski M, et al. Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation. Genes Dev. 2014;28:2219–32.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Viswanathan SR, Daley GQ, Gregory RI. Selective blockade of microRNA processing by Lin28. Science. 2008;320:97–100.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Wang S, Chim B, Su Y, Khil P, Wong M, Wang X, et al. Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. Genes Dev. 2019;33:1048–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Ali A, Bouma GJ, Anthony RV, Winger QA. The role of LIN28-let-7-ARID3B pathway in placental development. Int J Mol Sci. 2020;21:3637.

  71. Lee S, Ko Y, Kim TJ. Homeostasis and regulation of autoreactive B cells. Cell Mol Immunol. 2020;17:561–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Zhou Y, Li YS, Bandi SR, Tang L, Shinton SA, Hayakawa K, et al. Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a. J Exp Med. 2015;212:569–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Hayakawa K, Hardy RR, Honda M, Herzenberg LA, Steinberg AD, Herzenberg LA. Ly-1 B cells: functionally distinct lymphocytes that secrete IgM autoantibodies. Proc Natl Acad Sci USA. 1984;81:2494–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Hardy RR, Hayakawa K. Perspectives on fetal derived CD5+ B1 B cells. Eur J Immunol. 2015;45:2978–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Xu X, Deobagkar-Lele M, Bull KR, Crockford TL, Mead AJ, Cribbs AP, et al. An ontogenetic switch drives the positive and negative selection of B cells. Proc Natl Acad Sci USA. 2020;117:3718–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Yuan J, Nguyen CK, Liu X, Kanellopoulou C, Muljo SA. Lin28b reprograms adult bone marrow hematopoietic progenitors to mediate fetal-like lymphopoiesis. Science. 2012;335:1195–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Hayakawa K, Li YS, Shinton SA, Bandi SR, Formica AM, Brill-Dashoff J, et al. Crucial role of increased Arid3a at the Pre-B and immature B cell stages for B1a cell generation. Front Immunol. 2019;10:457.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Habir K, Aeinehband S, Wermeling F, Malin S. A role for the transcription factor Arid3a in mouse B2 lymphocyte expansion and peritoneal B1a generation. Front Immunol. 2017;8:1387.

    Article  PubMed  PubMed Central  Google Scholar 

  79. Ratliff ML, Templeton TD, Ward JM, Webb CF. The bright side of hematopoiesis: regulatory roles of ARID3a/Bright in human and mouse hematopoiesis. Front Immunol. 2014;5:113.

    Article  PubMed  PubMed Central  Google Scholar 

  80. Webb CF, Bryant J, Popowski M, Allred L, Kim D, Harriss J, et al. The ARID family transcription factor bright is required for both hematopoietic stem cell and B lineage development. Mol Cell Biol. 2011;31:1041–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Schmidt C, Kim D, Ippolito GC, Naqvi HR, Probst L, Mathur S, et al. Signalling of the BCR is regulated by a lipid rafts-localised transcription factor, Bright. EMBO J. 2009;28:711–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Pan C, Baumgarth N, Parnes JR. CD72-deficient mice reveal nonredundant roles of CD72 in B cell development and activation. Immunity. 1999;11:495–506.

    Article  CAS  PubMed  Google Scholar 

  83. Hoffmann A, Kerr S, Jellusova J, Zhang J, Weisel F, Wellmann U, et al. Siglec-G is a B1 cell-inhibitory receptor that controls expansion and calcium signaling of the B1 cell population. Nat Immunol. 2007;8:695–704.

    Article  CAS  PubMed  Google Scholar 

  84. Masmoudi H, Mota-Santos T, Huetz F, Coutinho A, Cazenave PA. All T15 Id-positive antibodies (but not the majority of VHT15+ antibodies) are produced by peritoneal CD5+ B lymphocytes. Int Immunol. 1990;2:515–20.

    Article  CAS  PubMed  Google Scholar 

  85. Yi M, Wu P, Trevorrow KW, Claflin L, Garrard WT. Evidence that the Igkappa gene MAR regulates the probability of premature V-J joining and somatic hypermutation. J Immunol. 1999;162:6029–39.

    Article  CAS  PubMed  Google Scholar 

  86. Hale MA, Garrard WT. A targeted kappa immunoglobulin gene containing a deletion of the nuclear matrix association region exhibits spontaneous hyper-recombination in pre-B cells. Mol Immunol. 1998;35:609–20.

    Article  CAS  PubMed  Google Scholar 

  87. Fernández LA, Winkler M, Grosschedl R. Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy. Mol Cell Biol. 2001;21:196–208.

    Article  PubMed  PubMed Central  Google Scholar 

  88. Su TT, Rawlings DJ. Transitional B lymphocyte subsets operate as distinct checkpoints in murine splenic B cell development. J Immunol. 2002;168:2101–10.

    Article  CAS  PubMed  Google Scholar 

  89. Shankar M, Nixon JC, Maier S, Workman J, Farris AD, Webb CF. Anti-nuclear antibody production and autoimmunity in transgenic mice that overexpress the transcription factor Bright. J Immunol. 2007;178:2996–3006.

    Article  CAS  PubMed  Google Scholar 

  90. Oldham AL, Miner CA, Wang HC, Webb CF. The transcription factor Bright plays a role in marginal zone B lymphocyte development and autoantibody production. Mol Immunol. 2011;49:367–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Ratliff ML, Garton J, James JA, Webb CF. ARID3a expression in human hematopoietic stem cells is associated with distinct gene patterns in aged individuals. Immun Ageing. 2020;17:24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ratliff ML, Mishra M, Frank MB, Guthridge JM, Webb CF. The transcription factor ARID3a is important for in vitro differentiation of human hematopoietic progenitors. J Immunol. 2016;196:614–23.

    Article  CAS  PubMed  Google Scholar 

  93. Hardy RR, Hayakawa K, Shimizu M, Yamasaki K, Kishimoto T. Rheumatoid factor secretion from human Leu-1+ B cells. Science. 1987;236:81–3.

    Article  CAS  PubMed  Google Scholar 

  94. Fazel-Najafabadi M, Rallabandi HR, Singh MK, Maiti GP, Morris J, Looger LL, et al. Discovery and functional characterization of two regulatory variants underlying lupus susceptibility at 2p13.1. Genes. 2022;13:1016.

  95. Amarilyo G, La Cava A. miRNA in systemic lupus erythematosus. Clin Immunol. 2012;144:26–31.

    Article  CAS  PubMed  Google Scholar 

  96. Molano-González N, Rojas M, Monsalve DM, Pacheco Y, Acosta-Ampudia Y, Rodríguez Y, et al. Cluster analysis of autoimmune rheumatic diseases based on autoantibodies. New insights for polyautoimmunity. J Autoimmun. 2019;98:24–32.

    Article  PubMed  Google Scholar 

  97. Ratliff ML, Ward JM, Merrill JT, James JA, Webb CF. Differential expression of the transcription factor ARID3a in lupus patient hematopoietic progenitor cells. J Immunol. 2015;194:940–9.

    Article  CAS  PubMed  Google Scholar 

  98. Kil LP, de Bruijn MJ, van Nimwegen M, Corneth OB, van Hamburg JP, Dingjan GM, et al. Btk levels set the threshold for B-cell activation and negative selection of autoreactive B cells in mice. Blood. 2012;119:3744–56.

    Article  CAS  PubMed  Google Scholar 

  99. Garton J, Barron MD, Ratliff ML, Webb CF. New frontiers: ARID3a in SLE. Cells. 2019;8:1136.

  100. Rosenwald A, Wright G, Leroy K, Yu X, Gaulard P, Gascoyne RD, et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J Exp Med. 2003;198:851–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–11.

    Article  CAS  PubMed  Google Scholar 

  102. Peeper DS, Shvarts A, Brummelkamp T, Douma S, Koh EY, Daley GQ, et al. A functional screen identifies hDRIL1 as an oncogene that rescues RAS-induced senescence. Nat Cell Biol. 2002;4:148–53.

    Article  CAS  PubMed  Google Scholar 

  103. Fukuyo Y, Mogi K, Tsunematsu Y, Nakajima T. E2FBP1/hDril1 modulates cell growth through downregulation of promyelocytic leukemia bodies. Cell Death Differ. 2004;11:747–59.

    Article  CAS  PubMed  Google Scholar 

  104. Ratliff ML, Garton J, Garman L, Barron MD, Georgescu C, White KA, et al. ARID3a gene profiles are strongly associated with human interferon alpha production. J Autoimmun. 2019;96:158–67.

    Article  CAS  PubMed  Google Scholar 

  105. Garcia-Romo GS, Caielli S, Vega B, Connolly J, Allantaz F, Xu Z, et al. Netting neutrophils are major inducers of type I IFN production in pediatric systemic lupus erythematosus. Sci Transl Med. 2011;3:73ra20.

    Article  PubMed  PubMed Central  Google Scholar 

  106. Qiu F, Tang R, Zuo X, Shi X, Wei Y, Zheng X, et al. A genome-wide association study identifies six novel risk loci for primary biliary cholangitis. Nat Commun. 2017;8:14828.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Mehrvarz Sarshekeh A, Alshenaifi J, Roszik J, Manyam GC, Advani SM, Katkhuda R, et al. ARID1A mutation may define an immunologically active subgroup in patients with microsatellite stable colorectal cancer. Clin Cancer Res. 2021;27:1663–70.

    Article  PubMed  PubMed Central  Google Scholar 

  108. Sayegh J, Cao J, Zou MR, Morales A, Blair LP, Norcia M, et al. Identification of small molecule inhibitors of Jumonji AT-rich interactive domain 1B (JARID1B) histone demethylase by a sensitive high throughput screen. J Biol Chem. 2013;288:9408–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Wang L, Chang J, Varghese D, Dellinger M, Kumar S, Best AM, et al. A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth. Nat Commun. 2013;4:2035.

    Article  PubMed  Google Scholar 

  110. Prieur A, Nacerddine K, van Lohuizen M, Peeper DS. SUMOylation of DRIL1 directs its transcriptional activity towards leukocyte lineage-specific genes. PLoS One. 2009;4:e5542.

    Article  PubMed  PubMed Central  Google Scholar 

  111. Lin L, Zhou Z, Zheng L, Alber S, Watkins S, Ray P, et al. Cross talk between Id1 and its interactive protein Dril1 mediate fibroblast responses to transforming growth factor-beta in pulmonary fibrosis. Am J Pathol. 2008;173:337–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Hassin O, Oren M. Drugging p53 in cancer: one protein, many targets. Nat Rev Drug Discov. 2023;22:127–44.

    Article  CAS  PubMed  Google Scholar 

  113. Crooke ST, Baker BF, Crooke RM, Liang XH. Antisense technology: an overview and prospectus. Nat Rev Drug Discov. 2021;20:427–53.

    Article  CAS  PubMed  Google Scholar 

  114. Wu JN, Roberts CW. ARID1A mutations in cancer: another epigenetic tumor suppressor? Cancer Discov. 2013;3:35–43.

    Article  CAS  PubMed  Google Scholar 

  115. Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, et al. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat Genet. 2012;44:376–8.

    Article  CAS  PubMed  Google Scholar 

  116. Santen GW, Aten E, Sun Y, Almomani R, Gilissen C, Nielsen M, et al. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome. Nat Genet. 2012;44:379–80.

    Article  CAS  PubMed  Google Scholar 

  117. Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet. 2014;46:1063–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. The Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature. 2015;519:223–8.

  119. Oba A, Shimada S, Akiyama Y, Nishikawaji T, Mogushi K, Ito H, et al. ARID2 modulates DNA damage response in human hepatocellular carcinoma cells. J Hepatol. 2017;66:942–51.

    Article  CAS  PubMed  Google Scholar 

  120. Wang X, Wang Y, Fang Z, Wang H, Zhang J, Zhang L, et al. Targeting HSPA1A in ARID2-deficient lung adenocarcinoma. Natl Sci Rev. 2021;8:nwab014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Bögershausen N, Wollnik B. Mutational landscapes and phenotypic spectrum of SWI/SNF-related intellectual disability disorders. Front Mol Neurosci. 2018;11:252.

    Article  PubMed  PubMed Central  Google Scholar 

  122. Numata S, Claudio PP, Dean C, Giordano A, Croce CM. Bdp, a new member of a family of DNA-binding proteins, associates with the retinoblastoma gene product. Cancer Res. 1999;59:3741–7.

    CAS  PubMed  Google Scholar 

  123. Wu MY, Tsai TF, Beaudet AL. Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Genes Dev. 2006;20:2859–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Wu RC, Young IC, Chen YF, Chuang ST, Toubaji A, Wu MY. Identification of the PTEN-ARID4B-PI3K pathway reveals the dependency on ARID4B by PTEN-deficient prostate cancer. Nat Commun. 2019;10:4332.

    Article  PubMed  PubMed Central  Google Scholar 

  125. Xu H, Cheng C, Devidas M, Pei D, Fan Y, Yang W, et al. ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. J Clin Oncol. 2012;30:751–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, et al. The emerging role of KDM5A in human cancer. J Hematol Oncol. 2021;14:30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Schmitz SU, Albert M, Malatesta M, Morey L, Johansen JV, Bak M, et al. Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J. 2011;30:4586–600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature. 2010;463:360–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell. 2007;128:1077–88.

    Article  CAS  PubMed  Google Scholar 

  130. Lee MG, Norman J, Shilatifard A, Shiekhattar R. Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell. 2007;128:877–87.

    Article  CAS  PubMed  Google Scholar 

  131. Kasinath V, Beck C, Sauer P, Poepsel S, Kosmatka J, Faini M, et al. JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Science. 2021;371:eabc3393.

  132. Gong W, Liang Q, Tong Y, Perrett S, Feng Y. Structural insight into chromatin recognition by multiple domains of the tumor suppressor RBBP1. J Mol Biol. 2021;433:167224.

    Article  CAS  PubMed  Google Scholar 

  133. Cai S, Zhu L, Zhang Z, Chen Y. Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling. Biochemistry. 2007;46:4943–50.

    Article  CAS  PubMed  Google Scholar 

  134. Labadie SS, Dragovich PS, Cummings RT, Deshmukh G, Gustafson A, Han N, et al. Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors. Bioorg Med Chem Lett. 2016;26:4492–6.

    Article  CAS  PubMed  Google Scholar 

  135. Liang J, Labadie S, Zhang B, Ortwine DF, Patel S, Vinogradova M, et al. From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors. Bioorg Med Chem Lett. 2017;27:2974–81.

    Article  CAS  PubMed  Google Scholar 

  136. Koehler C, Bishop S, Dowler EF, Schmieder P, Diehl A, Oschkinat H, et al. Backbone and sidechain 1H, 13C and 15N resonance assignments of the Bright/ARID domain from the human JARID1C (SMCX) protein. Biomol NMR Assign. 2008;2:9–11.

    Article  CAS  PubMed  Google Scholar 

  137. Justin N, Zhang Y, Tarricone C, Martin SR, Chen S, Underwood E, et al. Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Nat Commun. 2016;7:11316.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was partially supported by Ministry of Science and Technology (China) grants (2018YFA0507002 to HEX); Shanghai Municipal Science and Technology Major Project (2019SHZDZX02 to HEX); Shanghai Municipal Science and Technology Major Project (HEX); CAS Strategic Priority Research Program (XDB37030103 to HEX); the National Natural Science Foundation of China (32130022 and 82121005 to HEX, 81830016, 81771732 and 81620108002 to XM). We have used chatGPT to help the authors correct language and grammatic errors.

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Correspondence to Cheng-cen Guo, H. Eric Xu or Xiong Ma.

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HEX is the founder and chairman of board of Cascade Pharmaceutics. CCG and XM do not have conflicts of interest to declare.

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Guo, Cc., Xu, H.E. & Ma, X. ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery. Acta Pharmacol Sin 44, 2139–2150 (2023). https://doi.org/10.1038/s41401-023-01134-2

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