Epigenetic regulation of T cell development

References

• Dutta A, Zhao B, Love PE. New insights into TCR β-selection. Trends Immunol. 2021;42(8):735–750. doi:10.1016/j.it.2021.06.005.
   PubMed Web of Science ®Google Scholar
• Shortman K, Egerton M, Spangrude GJ, et al. The generation and fate of thymocytes. Semin Immunol. 1990;2(1):3–12.
   PubMedGoogle Scholar
• Michie AM, Zúñiga-Pflücker JC. Regulation of thymocyte differentiation: pre-TCR signals and beta-selection. Semin Immunol. 2002;14(5):311–323. doi:10.1016/S1044-5323(02)00064-7.
   PubMed Web of Science ®Google Scholar
• Zhao B, Yoganathan K, Li LQi, et al. Notch and the pre-TCR coordinate thymocyte proliferation by induction of the SCF subunits Fbxl1 and Fbxl12. Nat Immunol. 2019;20(10):1381–1392. doi:10.1038/s41590-019-0469-z.
   PubMed Web of Science ®Google Scholar
• Hayes SM, Laird RM, Love PE. Beyond alphabeta/gammadelta lineage commitment: TCR signal strength regulates gammadelta T cell maturation and effector fate. Semin Immunol. 2010;22(4):247–251. doi:10.1016/j.smim.2010.04.006.
   PubMed Web of Science ®Google Scholar
• Kumar BV, Connors TJ, Farber DL. Human T cell development, localization, and function throughout life. Immunity. 2018;48(2):202–213. doi:10.1016/j.immuni.2018.01.007.
   PubMed Web of Science ®Google Scholar
• Eriksson J, D’Angelo W, Badylak SF. Common Challenges in Tissue Regeneration. Epigenetics and Regeneration; 2019. p. 217–229.
   Google Scholar
• Schmidl C, Delacher M, Huehn J, et al. Epigenetic mechanisms regulating T-cell responses. J Allergy Clin Immunol. 2018;142(3):728–743. doi:10.1016/j.jaci.2018.07.014.
   PubMed Web of Science ®Google Scholar
• Leoni C, Vincenzetti L, Emming S, et al. Epigenetics of T lymphocytes in health and disease. Swiss Med Wkly. 2015;145:w14191. doi:10.4414/smw.2015.14191.
   PubMed Web of Science ®Google Scholar
• Lyu J, Wang L, Lu L. Thymocyte selection: from signaling to epigenetic regulation. Adv Immunol. 2019;144:1–22.
   PubMed Web of Science ®Google Scholar
• Yoon B-H, Kim M, Kim M-H, et al. Dynamic transcriptome, DNA methylome, and DNA hydroxymethylome networks during T-cell lineage commitment. Mol Cells. 2018;41(11):953–963.
   PubMed Web of Science ®Google Scholar
• Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150(1):12–27. doi:10.1016/j.cell.2012.06.013.
   PubMed Web of Science ®Google Scholar
• Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell. 2007;128(4):707–719. doi:10.1016/j.cell.2007.01.015.
   PubMed Web of Science ®Google Scholar
• Cheutin T, McNairn AJ, Jenuwein T, et al. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science. 2003;299(5607):721–725. doi:10.1126/science.1078572.
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–492. doi:10.1038/nrg3230.
   PubMed Web of Science ®Google Scholar
• Yin Y, Morgunova E, Jolma A, et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 2017 May 5;356(6337). doi:10.1126/science.aaj2239.
   Web of Science ®Google Scholar
• Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. Chembiochem. 2011;12(2):206–222. doi:10.1002/cbic.201000195.
   PubMed Web of Science ®Google Scholar
• Wu H, Zhang Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 2011;25(23):2436–2452. doi:10.1101/gad.179184.111.
   PubMed Web of Science ®Google Scholar
• Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013;502(7472):472–479. doi:10.1038/nature12750.
   PubMed Web of Science ®Google Scholar
• Turunen MP, Ylä-Herttuala S. Epigenetic regulation of key vascular genes and growth factors. Cardiovasc Res. 2011;90(3):441–446. doi:10.1093/cvr/cvr109.
   PubMed Web of Science ®Google Scholar
• Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293(5532):1074–1080. doi:10.1126/science.1063127.
   PubMed Web of Science ®Google Scholar
• Jambhekar A, Dhall A, Shi Y. Author Correction: Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol. 2020;21(1):59. doi:10.1038/s41580-019-0192-5.
   PubMed Web of Science ®Google Scholar
• Shi Y, Whetstine JR. Dynamic regulation of histone lysine methylation by demethylases. Mol Cell. 2007;25(1):1–14. doi:10.1016/j.molcel.2006.12.010.
   PubMed Web of Science ®Google Scholar
• Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693–705. doi:10.1016/j.cell.2007.02.005.
   PubMed Web of Science ®Google Scholar
• Breiling A, Sessa L, Orlando V. Biology of polycomb and trithorax group proteins. Int Rev Cytol. 2007;258:83–136.
   PubMedGoogle Scholar
• Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells. 2021;10(5):1074. doi:10.3390/cells10051074.
   PubMed Web of Science ®Google Scholar
• Chittock EC, Latwiel S, Miller TCR, et al. Molecular architecture of polycomb repressive complexes. Biochem Soc Trans. 2017;45(1):193–205. doi:10.1042/BST20160173.
   PubMedGoogle Scholar
• Shi Y, Lan F, Matson C, et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004;119(7):941–953. doi:10.1016/j.cell.2004.12.012.
   PubMed Web of Science ®Google Scholar
• Li Y, Deng C, Hu X, et al. Dynamic interaction between TAL1 oncoprotein and LSD1 regulates TAL1 function in hematopoiesis and leukemogenesis. Oncogene. 2012;31(48):5007–5018. doi:10.1038/onc.2012.8.
   PubMed Web of Science ®Google Scholar
• Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep. 2015;16(12):1620–1639. doi:10.15252/embr.201541113.
   PubMed Web of Science ®Google Scholar
• Ropero S, Esteller M. The role of histone deacetylases (HDACs) in human cancer. Mol Oncol. 2007;1(1):19–25. doi:10.1016/j.molonc.2007.01.001.
   PubMed Web of Science ®Google Scholar
• Josling GA, Selvarajah SA, Petter M, et al. The role of bromodomain proteins in regulating gene expression. Genes (Basel). 2012;3(2):320–343. doi:10.3390/genes3020320.
   PubMed Web of Science ®Google Scholar
• Park S-Y, Kim J-S. A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med. 2020;52(2):204–212. doi:10.1038/s12276-020-0382-4.
   PubMed Web of Science ®Google Scholar
• Foglizzo M, Middleton AJ, Burgess AE, et al. A bidentate polycomb repressive-deubiquitinase complex is required for efficient activity on nucleosomes. Nat Commun. 2018;9(1). doi:10.1038/s41467-018-06186-1.
   PubMedGoogle Scholar
• Vissers JH, Nicassio F, van Lohuizen M, et al. The many faces of ubiquitinated histone H2A: insights from the DUBs. Cell Div. 2008;3(1):8. doi:10.1186/1747-1028-3-8.
   PubMedGoogle Scholar
• Sundaramoorthy R, Owen-Hughes T. Chromatin remodelling comes into focus. F1000Res. 2020;9:1011. doi:10.12688/f1000research.21933.1.
   Google Scholar
• Wang GG, Allis CD, Chi P. Chromatin remodeling and cancer, part II: ATP-dependent chromatin remodeling. Trends Mol Med. 2007;13(9):373–380. doi:10.1016/j.molmed.2007.07.004.
   PubMed Web of Science ®Google Scholar
• Stengel KR, Zhao Y, Klus NJ, et al. Histone deacetylase 3 is required for efficient T cell development. Mol Cell Biol. 2015;35(22):3854–3865. doi:10.1128/MCB.00706-15.
   PubMed Web of Science ®Google Scholar
• Philips RL, Lee J-H, Gaonkar K, et al. HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4 + CD8+ thymocytes for CD4-lineage commitment. eLife. 2019 Jan 18;8:e43821. doi:10.7554/eLife.43821.
   PubMed Web of Science ®Google Scholar
• Arenzana TL, Lianoglou S, Seki A, et al. Tumor suppressor BAP1 is essential for thymic development and proliferative responses of T lymphocytes. Sci Immunol. 2018 Apr 20;3(22):eaal1953. doi:10.1126/sciimmunol.aal1953.
   PubMed Web of Science ®Google Scholar
• Ji Z, Sheng Y, Miao J, et al. The histone methyltransferase Setd2 is indispensable for V(D)J recombination. Nat Commun. 2019;10(1). doi:10.1038/s41467-019-11282-x.
   Google Scholar
• Tate CM, Lee JH, Skalnik DG. CXXC finger protein 1 contains redundant functional domains that support embryonic stem cell cytosine methylation, histone methylation, and differentiation. Mol Cell Biol. 2009;29(14):3817–3831. doi:10.1128/MCB.00243-09.
   PubMed Web of Science ®Google Scholar
• Cao W, Guo J, Wen X, et al. CXXC finger protein 1 is critical for T-cell intrathymic development through regulating H3K4 trimethylation. Nat Commun. 2016;7(1):11687. doi:10.1038/ncomms11687.
   PubMedGoogle Scholar
• Shilatifard A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem. 2012;81:65–95. doi:10.1146/annurev-biochem-051710-134100.
   PubMed Web of Science ®Google Scholar
• Stamos DB, et al. The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. J Exp Med. 2021 Dec 6;218(12):e20202012. doi:10.1084/jem.20202012.
   PubMed Web of Science ®Google Scholar
• Manna S, Kim JK, Baugé C, et al. Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation. Nat Commun. 2015;6(1):8152. doi:10.1038/ncomms9152.
   PubMedGoogle Scholar
• Carey BW, Finley LWS, Cross JR, et al. Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature. 2015;518(7539):413–416. doi:10.1038/nature13981.
   PubMed Web of Science ®Google Scholar
• Lee PP, Fitzpatrick DR, Beard C, et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity. 2001;15(5):763–774. doi:10.1016/S1074-7613(01)00227-8.
   PubMed Web of Science ®Google Scholar
• Ji H, Ehrlich LIR, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010;467(7313):338–342. doi:10.1038/nature09367.
   PubMed Web of Science ®Google Scholar
• Correa LO, Jordan MS, Carty SA. DNA Methylation in T-Cell Development and Differentiation. Crit Rev Immunol. 2020;40(2):135–156. doi:10.1615/CritRevImmunol.2020033728.
   PubMed Web of Science ®Google Scholar
• Rodriguez RM, Suarez-Alvarez B, Mosén-Ansorena D, et al. Regulation of the transcriptional program by DNA methylation during human αβ T-cell development. Nucleic Acids Res. 2015;43(2):760–774. doi:10.1093/nar/gku1340.
   PubMed Web of Science ®Google Scholar
• Cheng L, Zhou K, Chen X, et al. Loss of MBD2 affects early T cell development by inhibiting the WNT signaling pathway. Exp Cell Res. 2021;398(1):112400. doi:10.1016/j.yexcr.2020.112400.
   PubMed Web of Science ®Google Scholar
• Bostick M, Kim JK, Estève P-O, et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science. 2007;317(5845):1760–1764. doi:10.1126/science.1147939.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Chen Y, Ma R, et al. UHRF1 controls thymocyte fate decisions through the epigenetic regulation of EGR1 expression. J Immunol. 2020;204(12):3248–3261. doi:10.4049/jimmunol.1901471.
   PubMed Web of Science ®Google Scholar
• Hayes SM, Li L, Love PE. TCR signal strength influences alphabeta/gammadelta lineage fate. Immunity. 2005;22(5):583–593. doi:10.1016/j.immuni.2005.03.014.
   PubMedGoogle Scholar
• Haks MC, Lefebvre JM, Lauritsen JPH, et al. Attenuation of gammadeltaTCR signaling efficiently diverts thymocytes to the alphabeta lineage. Immunity. 2005 May;22(5):595–606. doi:10.1016/j.immuni.2005.04.003.
   PubMed Web of Science ®Google Scholar
• Roels J, Kuchmiy A, De Decker M, et al. Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development. Nat Immunol. 2020;21(10):1280–1292. doi:10.1038/s41590-020-0747-9.
   PubMed Web of Science ®Google Scholar
• Kramer AC, Kothari A, Wilson WC, et al. Dnmt3a regulates T-cell development and suppresses T-ALL transformation. Leukemia. 2017;31(11):2479–2490. doi:10.1038/leu.2017.89.
   PubMed Web of Science ®Google Scholar
• Issuree PD, Day K, Au C, et al. Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development. Nat Commun. 2018;9(1). doi:10.1038/s41467-018-05834-w.
   PubMedGoogle Scholar
• Yoshida H, Lareau CA, Ramirez RN, Immunological Genome Project, et al. The cis-regulatory atlas of the mouse immune system. Cell. 2019 Feb 7;176(4):897–912.e20. doi:10.1016/j.cell.2018.12.036.
   PubMed Web of Science ®Google Scholar
• Johnson JL, Georgakilas G, Petrovic J, et al. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cells. Immunity. 2018;48(2):243–257.e10. doi:10.1016/j.immuni.2018.01.012.
   PubMed Web of Science ®Google Scholar
• Germar K, Dose M, Konstantinou T, et al. T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc Natl Acad Sci U S A. 2011;108(50):20060–20065. doi:10.1073/pnas.1110230108.
   PubMed Web of Science ®Google Scholar
• Weber BN, Chi AW-S, Chavez A, et al. A critical role for TCF-1 in T-lineage specification and differentiation. Nature. 2011;476(7358):63–68. doi:10.1038/nature10279.
   PubMed Web of Science ®Google Scholar
• Peirs S, Van der Meulen J, Van de Walle I, et al. Epigenetics in T-cell acute lymphoblastic leukemia. Immunol Rev. 2015;263(1):50–67. doi:10.1111/imr.12237.
   PubMed Web of Science ®Google Scholar