A precisely balanced activity of canonical Wnt signaling is essential for a number of biological processes and its perturbation leads to developmental defects or diseases. Here, we demonstrate that alternative isoforms of the KDM2A and KDM2B lysine demethylases have the ability to negatively regulate canonical Wnt signaling. These KDM2A and KDM2B isoforms (KDM2A-SF and KDM2B-SF) lack the N-terminal demethylase domain, but they still have the ability to bind to CpG islands in promoters and to interact with their protein partners via their other functional domains. We have observed that KDM2A-SF and KDM2B-SF bind to the promoters of axin 2 and cyclin D1, two canonical Wnt signaling target genes, and repress their activity. Moreover, KDM2A-SF and KDM2B-SF are both able to strongly repress a Wnt-responsive luciferase reporter. The transcriptional repression mediated by KDM2A-SF and KDM2B-SF, but also by KDM2A-LF, is dependent on their DNA binding domain, while the N-terminal demethylase domain is dispensable for this process. Surprisingly, KDM2B-LF is unable to repress both the endogenous promoters and the luciferase reporter. Finally, we show that both KDM2A-SF and KDM2B-SF are able to interact with TCF7L1, one of the transcriptional mediators of canonical Wnt signaling. KDM2A-SF and KDM2B-SF are thus likely to negatively affect the transcription of canonical Wnt signaling target genes by binding to their promoters and by interacting with TCF7L1 and other co-repressors.

Institute of Biology and Medical Genetics 1st Faculty of Medicine Charles University and General University Hospital Prague Czech Republic

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Vacik T, Ladinovic D, Raska I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus. 2018;9(1):431–41. 10.1080/19491034.2018.1498707 PubMed DOI PMC

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(7078):811–6. 10.1038/nature04433 PubMed DOI

Janzer A, Stamm K, Becker A, Zimmer A, Buettner R, Kirfel J. The H3K4me3 histone demethylase Fbxl10 is a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. J Biol Chem. 2012;287(37):30984–92. 10.1074/jbc.M112.341040 PubMed DOI PMC

Gates LA, Foulds CE, O'Malley BW. Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. Trends Biochem Sci. 2017;42(12):977–89. 10.1016/j.tibs.2017.10.004 PubMed DOI PMC

Black JC, Van Rechem C, Whetstine JR. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol Cell. 2012;48(4):491–507. 10.1016/j.molcel.2012.11.006 PubMed DOI PMC

Zaghi M, Broccoli V, Sessa A. H3K36 Methylation in Neural Development and Associated Diseases. Front Genet. 2019;10:1291 10.3389/fgene.2019.01291 PubMed DOI PMC

Dhar SS, Alam H, Li N, Wagner KW, Chung J, Ahn YW, et al. Transcriptional repression of histone deacetylase 3 by the histone demethylase KDM2A is coupled to tumorigenicity of lung cancer cells. J Biol Chem. 2014;289(11):7483–96. 10.1074/jbc.M113.521625 PubMed DOI PMC

Wagner KW, Alam H, Dhar SS, Giri U, Li N, Wei Y, et al. KDM2A promotes lung tumorigenesis by epigenetically enhancing ERK1/2 signaling. J Clin Invest. 2013;123(12):5231–46. 10.1172/JCI68642 PubMed DOI PMC

He J, Kallin EM, Tsukada Y, Zhang Y. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat Struct Mol Biol. 2008;15(11):1169–75. 10.1038/nsmb.1499 PubMed DOI PMC

Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. eLife. 2012;1:e00205 10.7554/eLife.00205 PubMed DOI PMC

Borgel J, Tyl M, Schiller K, Pusztai Z, Dooley CM, Deng W, et al. KDM2A integrates DNA and histone modification signals through a CXXC/PHD module and direct interaction with HP1. Nucleic Acids Res. 2017;45(3):1114–29. 10.1093/nar/gkw979 PubMed DOI PMC

Ladinovic D, Novotna J, Jaksova S, Raska I, Vacik T. A demethylation deficient isoform of the lysine demethylase KDM2A interacts with pericentromeric heterochromatin in an HP1a-dependent manner. Nucleus. 2017;8(5):563–72. 10.1080/19491034.2017.1342915 PubMed DOI PMC

Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, Basrur V, et al. KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle. 2008;7(22):3539–47. 10.4161/cc.7.22.7062 PubMed DOI PMC

Lu L, Gao Y, Zhang Z, Cao Q, Zhang X, Zou J, et al. Kdm2a/b Lysine Demethylases Regulate Canonical Wnt Signaling by Modulating the Stability of Nuclear beta-Catenin. Dev Cell. 2015;33(6):660–74. 10.1016/j.devcel.2015.04.006 PubMed DOI

Lu T, Jackson MW, Wang B, Yang M, Chance MR, Miyagi M, et al. Regulation of NF-kappaB by NSD1/FBXL11-dependent reversible lysine methylation of p65. Proc Natl Acad Sci U S A. 2010;107(1):46–51. 10.1073/pnas.0912493107 PubMed DOI PMC

Nusse R, Clevers H. Wnt/beta-Catenin Signaling, Disease, and Emerging Therapeutic Modalities. Cell. 2017;169(6):985–99. 10.1016/j.cell.2017.05.016 PubMed DOI

Anastas JN, Moon RT. WNT signalling pathways as therapeutic targets in cancer. Nat Rev Cancer. 2013;13(1):11–26. 10.1038/nrc3419 PubMed DOI

Clevers H, Nusse R. Wnt/beta-catenin signaling and disease. Cell. 2012;149(6):1192–205. 10.1016/j.cell.2012.05.012 PubMed DOI

MacDonald BT, Tamai K, He X. Wnt/beta-catenin signaling: components, mechanisms, and diseases. Dev Cell. 2009;17(1):9–26. 10.1016/j.devcel.2009.06.016 PubMed DOI PMC

Sokol SY. Maintaining embryonic stem cell pluripotency with Wnt signaling. Development. 2011;138(20):4341–50. 10.1242/dev.066209 PubMed DOI PMC

Cadigan KM, Peifer M. Wnt signaling from development to disease: insights from model systems. Cold Spring Harbor perspectives in biology. 2009;1(2):a002881 10.1101/cshperspect.a002881 PubMed DOI PMC

Stamos JL, Weis WI. The beta-catenin destruction complex. Cold Spring Harbor perspectives in biology. 2013;5(1):a007898 10.1101/cshperspect.a007898 PubMed DOI PMC

Fagotto F. Looking beyond the Wnt pathway for the deep nature of beta-catenin. EMBO Rep. 2013;14(5):422–33. 10.1038/embor.2013.45 PubMed DOI PMC

Kawakami E, Tokunaga A, Ozawa M, Sakamoto R, Yoshida N. The histone demethylase Fbxl11/Kdm2a plays an essential role in embryonic development by repressing cell-cycle regulators. Mech Dev. 2015;135:31–42. 10.1016/j.mod.2014.10.001 PubMed DOI

Boulard M, Edwards JR, Bestor TH. Abnormal X chromosome inactivation and sex-specific gene dysregulation after ablation of FBXL10. Epigenetics & chromatin. 2016;9(22):22. PubMed PMC

Andricovich J, Kai Y, Peng W, Foudi A, Tzatsos A. Histone demethylase KDM2B regulates lineage commitment in normal and malignant hematopoiesis. J Clin Invest. 2016;126(3):905–20. 10.1172/JCI84014 PubMed DOI PMC

Fukuda T, Tokunaga A, Sakamoto R, Yoshida N. Fbxl10/Kdm2b deficiency accelerates neural progenitor cell death and leads to exencephaly. Mol Cell Neurosci. 2011;46(3):614–24. 10.1016/j.mcn.2011.01.001 PubMed DOI

Vacik T, Stubbs JL, Lemke G. A novel mechanism for the transcriptional regulation of Wnt signaling in development. Genes Dev. 2011;25(17):1783–95. 10.1101/gad.17227011 PubMed DOI PMC

Tseng AS, Engel FB, Keating MT. The GSK-3 inhibitor BIO promotes proliferation in mammalian cardiomyocytes. Chemistry & biology. 2006;13(9):957–63. PubMed

Sato N, Meijer L, Skaltsounis L, Greengard P, Brivanlou AH. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nature medicine. 2004;10(1):55–63. 10.1038/nm979 PubMed DOI

Meijer L, Skaltsounis AL, Magiatis P, Polychronopoulos P, Knockaert M, Leost M, et al. GSK-3-selective inhibitors derived from Tyrian purple indirubins. Chemistry & biology. 2003;10(12):1255–66. PubMed

Cohen P, Goedert M. GSK3 inhibitors: development and therapeutic potential. Nat Rev Drug Discov. 2004;3(6):479–87. 10.1038/nrd1415 PubMed DOI

Patel P, Woodgett JR. Glycogen Synthase Kinase 3: A Kinase for All Pathways? Curr Top Dev Biol. 2017;123:277–302. 10.1016/bs.ctdb.2016.11.011 PubMed DOI

Hur EM, Zhou FQ. GSK3 signalling in neural development. Nat Rev Neurosci. 2010;11(8):539–51. 10.1038/nrn2870 PubMed DOI PMC

Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010;38(2):179–90. 10.1016/j.molcel.2010.04.009 PubMed DOI PMC

He TC, Sparks AB, Rago C, Hermeking H, Zawel L, da Costa LT, et al. Identification of c-MYC as a target of the APC pathway. Science. 1998;281(5382):1509–12. 10.1126/science.281.5382.1509 PubMed DOI

Lustig B, Jerchow B, Sachs M, Weiler S, Pietsch T, Karsten U, et al. Negative feedback loop of Wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Mol Cell Biol. 2002;22(4):1184–93. 10.1128/mcb.22.4.1184-1193.2002 PubMed DOI PMC

Jho EH, Zhang T, Domon C, Joo CK, Freund JN, Costantini F. Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol Cell Biol. 2002;22(4):1172–83. 10.1128/mcb.22.4.1172-1183.2002 PubMed DOI PMC

Tetsu O, McCormick F. Beta-catenin regulates expression of cyclin D1 in colon carcinoma cells. Nature. 1999;398(6726):422–6. 10.1038/18884 PubMed DOI

Shtutman M, Zhurinsky J, Simcha I, Albanese C, D'Amico M, Pestell R, et al. The cyclin D1 gene is a target of the beta-catenin/LEF-1 pathway. Proc Natl Acad Sci U S A. 1999;96(10):5522–7. 10.1073/pnas.96.10.5522 PubMed DOI PMC

Zhou Z, Yang X, He J, Liu J, Wu F, Yu S, et al. Kdm2b Regulates Somatic Reprogramming through Variant PRC1 Complex-Dependent Function. Cell reports. 2017;21(8):2160–70. 10.1016/j.celrep.2017.10.091 PubMed DOI

He J, Shen L, Wan M, Taranova O, Wu H, Zhang Y. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat Cell Biol. 2013;15(4):373–84. 10.1038/ncb2702 PubMed DOI PMC

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006. 10.1101/gr.229102 PubMed DOI PMC

Lysine Demethylase KDM2A Promotes Proteasomal Degradation of TCF/LEF Transcription Factors in a Neddylation-Dependent Manner