Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor–DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Hosokawa, H. & Rothenberg, E. V. Cytokines, transcription factors, and the initiation of T-cell development. Cold Spring Harb. Perspect. Biol. 10, a028621 (2018).
Yui, M. A. & Rothenberg, E. V. Developmental gene networks: a triathlon on the course to T cell identity. Nat. Rev. Immunol. 14, 529–545 (2014).
Lu, M. et al. The earliest thymic progenitors in adults are restricted to T, NK, and dendritic cell lineage and have a potential to form more diverse TCRβ chains than fetal progenitors. J. Immunol. 175, 5848–5856 (2005).
Singer, A., Adoro, S. & Park, J. H. Lineage fate and intense debate: myths, models and mechanisms of CD4− versus CD8-lineage choice. Nat. Rev. Immunol. 8, 788–801 (2008).
Desiderio, S. Temporal and spatial regulatory functions of the V(D)J recombinase. Semin. Immunol. 22, 362–369 (2010).
Rothenberg, E. V., Moore, J. E. & Yui, M. A. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 8, 9–21 (2008).
Yang, Q., Jeremiah Bell, J. & Bhandoola, A. T-cell lineage determination. Immunol. Rev. 238, 12–22 (2010).
Romanoski, C. E., Link, V. M., Heinz, S. & Glass, C. K. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol. 36, 507–518 (2015).
Laiosa, C. V., Stadtfeld, M. & Graf, T. Determinants of lymphoid-myeloid lineage diversification. Annu. Rev. Immunol. 24, 705–738 (2006).
Takahashi, K. & Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17, 183–193 (2016).
Schebesta, A. et al. Transcription factor Pax5 activates the chromatin of key genes involved in B cell signaling, adhesion, migration, and immune function. Immunity 27, 49–63 (2007).
Lin, Y. C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat. Immunol. 11, 635–643 (2010).
Seo, W. & Taniuchi, I. Transcriptional regulation of early T-cell development in the thymus. Eur. J. Immunol. 46, 531–538 (2016).
Thompson, P. K. & Zúñiga-Pflücker, J. C. On becoming a T cell, a convergence of factors kick it up a Notch along the way. Semin. Immunol. 23, 350–359 (2011).
Rothenberg, E. V., Ungerback, J. & Champhekar, A. Forging T-lymphocyte identity: intersecting networks of transcriptional control. Adv. Immunol. 129, 109–174 (2016).
Zhou, W. et al. Single-cell analysis reveals regulatory gene expression dynamics leading to lineage commitment in early T cell development. Cell Syst. 9, 321–337 e9 (2019). This study focuses on patterns of transcription factor expression in the earliest stages of T cell differentiation and their relationship to developmental potentials at the single-cell level using single-molecule fluorescence in situ hybridization and RNA sequencing for high-sensitivity quantitation of the expression of multiple transcription factor genes in the same single cells.
Cleveland, S. M. et al. Lmo2 induces hematopoietic stem cell-like features in T-cell progenitor cells prior to leukemia. Stem Cells 31, 882–894 (2013).
Hu, G. et al. Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells. Immunity 48, 227–242 e8 (2018). Revealing major changes in chromatin organization during commitment, this study shows that PU.1 motifs predominate in chromatin regions that are open early in pro-T cells. Then PU.1 occupancy gives way to BCL-11B occupancy of open sites across the genome, with evidence that BCL-11B is important as a factor associated with genomic loops in T lineage cells.
Ungerbäck, J. et al. Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1). Genome Res. 28, 1508–1519 (2018). This study uses a motif quality metric for a global dissection of how PU.1 functions in open chromatin maintenance, pioneer-like activity and gene regulation in early pro-T cells. It shows that PU.1 respects chromatin constraints but can bind to closed sites if they are of sufficiently high affinity.
Johnson, J. L. et al. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cells. Immunity 48, 243–257 e10 (2018). This study establishes TCF1 as a controller of open chromatin states in T lineage cells. The authors show enrichment of TCF1 motifs in T cell lineage-associated chromatin sites of two types: one set becoming accessible initially in ETPs, and a larger set becoming accessible around the time of or after commitment.
Lavaert, M. et al. Integrated scRNA-Seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes. Immunity 52, 1088–1104 e6 (2020).
Le, J. et al. Single-cell RNA-Seq mapping of human thymopoiesis reveals lineage specification trajectories and a commitment spectrum in T cell development. Immunity 52, 1105–1118 e9 (2020). Lavaert et al. (2020) and Le et al. provide complementary single-cell transcriptome analyses of pro-T cells in postnatal human thymus. Lavaert et al. focus on potential regulatory network connections, and Le et al. focus on lineage commitment. These two reports elegantly document broad similarities but some differences between early human and mouse stages.
Zhang, J. A., Mortazavi, A., Williams, B. A., Wold, B. J. & Rothenberg, E. V. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 149, 467–482 (2012).
Ji, H. et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467, 338–342 (2010).
Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912 e20 (2019). In this comprehensive survey, the authors show that enhancer activity correlates better with gene expression than promoter accessibility and that E protein and TCF family motifs predominate in enhancer sites that become accessible after T cell lineage commitment. A global analysis further relates specific factors to chromatin accessibility changes.
Radtke, F. et al. Deficient T cell fate specification in mice with an induced inactivation of Notch1. Immunity 10, 547–558 (1999).
Hozumi, K. et al. Delta-like 4 is indispensable in thymic environment specific for T cell development. J. Exp. Med. 205, 2507–2513 (2008).
Schmitt, T. M. & Zúñiga-Pflücker, J. C. Induction of T cell development from hematopoietic progenitor cells by Delta-like-1 in vitro. Immunity 17, 749–756 (2002).
Hozumi, K., Abe, N., Chiba, S., Hirai, H. & Habu, S. Active form of Notch members can enforce T lymphopoiesis on lymphoid progenitors in the monolayer culture specific for B cell development. J. Immunol. 170, 4973–4979 (2003).
Bray, S. J. Notch signalling: a simple pathway becomes complex. Nat. Rev. Mol. Cell. Biol. 7, 678–689 (2006).
Yashiro-Ohtani, Y., Ohtani, T. & Pear, W. S. Notch regulation of early thymocyte development. Semin. Immunol. 22, 261–269 (2010).
Ciofani, M. & Zúñiga-Pflücker, J. C. A survival guide to early T cell development. Immunol. Res. 34, 117–132 (2006).
Radtke, F., Macdonald, H. R. & Tacchini-Cottier, F. Regulation of innate and adaptive immunity by Notch. Nat. Rev. Immunol. 13, 427–437 (2013).
Mingueneau, M. et al. The transcriptional landscape of αβ T cell differentiation. Nat. Immunol. 14, 619–632 (2013).
De Obaldia, M. E. et al. T cell development requires constraint of the myeloid regulator C/EBP-α by the Notch target and transcriptional repressor Hes1. Nat. Immunol. 14, 1277–1284 (2013).
Wong, G. W., Knowles, G. C., Mak, T. W., Ferrando, A. A. & Zúñiga-Pflücker, J. C. HES1 opposes a PTEN-dependent check on survival, differentiation, and proliferation of TCRβ-selected mouse thymocytes. Blood. 120, 1439–1448 (2012).
Muñoz-Descalzo, S., de Navascues, J. & Martinez Arias, A. Wnt-Notch signalling: an integrated mechanism regulating transitions between cell states. Bioessays 34, 110–118 (2012).
Chen, E. L. Y., Thompson, P. K. & Zúñiga-Pflücker, J. C. RBPJ-dependent Notch signaling initiates the T cell program in a subset of thymus-seeding progenitors. Nat. Immunol. 20, 1456–1468 (2019). The authors develop a mouse strain in which the Notch-interacting transcription factor RBPJ can be deleted and then inducibly restored. The results confirm the need for sustained intrathymic signalling and show, unexpectedly, that a Notch signal via RBPJ needs to be delivered to bone marrow multipotent progenitors even before they reach the thymus.
Yu, V. W. et al. Specific bone cells produce DLL4 to generate thymus-seeding progenitors from bone marrow. J. Exp. Med. 212, 759–774 (2015).
Hirano, K. et al. Delta-like 4-mediated Notch signaling is required for early T-cell development in a three-dimensional thymic structure. Eur. J. Immunol. 45, 2252–2262 (2015).
Wolfer, A., Wilson, A., Nemir, M., MacDonald, H. R. & Radtke, F. Inactivation of Notch1 impairs VDJβ rearrangement and allows pre-TCR-independent survival of early αβ lineage thymocytes. Immunity 16, 869–879 (2002).
Romero-Wolf, M. et al. Notch2 complements Notch1 to mediate inductive signaling that initiates early T cell development. J. Cell Biol. 219, e202005093 (2020).
Yun, T. J. & Bevan, M. J. Notch-regulated ankyrin-repeat protein inhibits Notch1 signaling: multiple Notch1 signaling pathways involved in T cell development. J. Immunol. 170, 5834–5841 (2003).
Hosoya, T. et al. GATA-3 is required for early T lineage progenitor development. J. Exp. Med. 206, 2987–3000 (2009).
Germar, K. et al. T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc. Natl Acad. Sci. USA 108, 20060–20065 (2011).
Weber, B. N. et al. A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476, 63–68 (2011).
Del Real, M. M. & Rothenberg, E. V. Architecture of a lymphomyeloid developmental switch controlled by PU.1, Notch and Gata3. Development 140, 1207–1219 (2013).
Staal, F. J. T. & Sen, J. M. The canonical Wnt signaling pathway plays an important role in lymphopoiesis and hematopoiesis. Eur. J. Immunol. 38, 1788–1794 (2008).
Xu, Z. et al. Cutting edge: β-catenin-interacting Tcf1 isoforms are essential for thymocyte survival but dispensable for thymic maturation transitions. J. Immunol. 198, 3404–3409 (2017).
Jeannet, G. et al. Long-term, multilineage hematopoiesis occurs in the combined absence of β-catenin and γ-catenin. Blood. 111, 142–149 (2008).
Tiemessen, M. M. et al. The nuclear effector of Wnt-signaling, Tcf1, functions as a T-cell-specific tumor suppressor for development of lymphomas. PLoS Biol. 10, e1001430 (2012).
Yu, S. et al. The TCF-1 and LEF-1 transcription factors have cooperative and opposing roles in T cell development and malignancy. Immunity. 37, 813–826 (2012).
Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227–2241 (2011).
Emmanuel, A. O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4+CD8+ thymocytes. Nat. Immunol. 19, 1366–1378 (2018). The authors demonstrate the close cooperation between TCF1 and the bHLH factor HEB in establishing open chromatin and driving gene expression in DP thymocytes. TCF1 is shown to enhance the binding of HEB to many of its genomic sites and to promote HEB accumulation by blunting Notch signals that otherwise degrade HEB.
Frelin, C. et al. GATA-3 regulates the self-renewal of long-term hematopoietic stem cells. Nat. Immunol. 14, 1037–1044 (2013).
Tindemans, I., Serafini, N., Di Santo, J. P. & Hendriks, R. W. GATA-3 function in innate and adaptive immunity. Immunity. 41, 191–206 (2014).
Hasegawa, S. L. et al. Dosage-dependent rescue of definitive nephrogenesis by a distant Gata3 enhancer. Dev. Biol. 301, 568–577 (2007).
Lim, K. C. et al. Gata3 loss leads to embryonic lethality due to noradrenaline deficiency of the sympathetic nervous system. Nat. Genet. 25, 209–212 (2000).
Kouros-Mehr, H., Slorach, E. M., Sternlicht, M. D. & Werb, Z. GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland. Cell 127, 1041–1055 (2006).
Van Esch, H. et al. GATA3 haplo-insufficiency causes human HDR syndrome. Nature 406, 419–422 (2000).
Hozumi, K. et al. Notch signaling is necessary for GATA3 function in the initiation of T cell development. Eur. J. Immunol. 38, 977–985 (2008).
Garcia-Ojeda, M. E. et al. GATA-3 promotes T-cell specification by repressing B-cell potential in pro-T cells in mice. Blood 121, 1749–1759 (2013).
Scripture-Adams, D. D. et al. GATA-3 dose-dependent checkpoints in early T cell commitment. J. Immunol. 193, 3470–3491 (2014).
Hosoya, T. et al. Global dynamics of stage-specific transcription factor binding during thymocyte development. Sci. Rep. 8, 5605 (2018).
Ohmura, S. et al. Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs. J. Clin. Invest. 126, 865–878 (2016).
Xu, W. et al. E2A transcription factors limit expression of Gata3 to facilitate T lymphocyte lineage commitment. Blood 121, 1534–1542 (2013).
Taghon, T., Yui, M. A. & Rothenberg, E. V. Mast cell lineage diversion of T lineage precursors by the essential T cell transcription factor GATA-3. Nat. Immunol. 8, 845–855 (2007).
Hosoya, T., Maillard, I. & Engel, J. D. From the cradle to the grave: activities of GATA-3 throughout T-cell development and differentiation. Immunol. Rev. 238, 110–125 (2010).
Zhu, J. GATA3 regulates the development and functions of innate lymphoid cell subsets at multiple stages. Front. Immunol. 8, 1571 (2017).
Wei, G. et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35, 299–311 (2011).
Nakayama, T. et al. Th2 cells in health and disease. Annu. Rev. Immunol. 35, 53–84 (2017).
Furusawa, J. et al. Critical role of p38 and GATA3 in natural helper cell function. J. Immunol. 191, 1818–1826 (2013).
Hosokawa, H. et al. Methylation of Gata3 protein at Arg-261 regulates transactivation of the Il5 gene in T helper 2 cells. J. Biol. Chem. 290, 13095–13103 (2015).
Hosokawa, H. et al. Akt1-mediated Gata3 phosphorylation controls the repression of IFNγ in memory-type Th2 cells. Nat. Commun. 7, 11289 (2016).
Hosokawa, H. et al. Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity. Proc. Natl Acad. Sci. USA 110, 4691–4696 (2013).
Yamagata, T. et al. Acetylation of GATA-3 affects T-cell survival and homing to secondary lymphoid organs. EMBO J. 19, 4676–4687 (2000).
Buono, M. et al. A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors. Nat. Cell Biol. 18, 157–167 (2016).
Semerad, C. L., Mercer, E. M., Inlay, M. A., Weissman, I. L. & Murre, C. E2A proteins maintain the hematopoietic stem cell pool and promote the maturation of myelolymphoid and myeloerythroid progenitors. Proc. Natl Acad. Sci. USA 106, 1930–1935 (2009).
Yang, Q. et al. E47 controls the developmental integrity and cell cycle quiescence of multipotential hematopoietic progenitors. J. Immunol. 181, 5885–5894 (2008).
Dias, S., Mansson, R., Gurbuxani, S., Sigvardsson, M. & Kee, B. L. E2A proteins promote development of lymphoid-primed multipotent progenitors. Immunity 29, 217–227 (2008).
Miyazaki, M. et al. The E-Id protein axis specifies adaptive lymphoid cell identity and suppresses thymic innate lymphoid cell development. Immunity 46, 818–834 e4 (2017). E protein activity in ILCs is tightly inhibited by ID2. This study shows that inappropriate expression of Id2 or deletion of both Tcf3 and Tcf12 induces abnormal development of ILCs in the thymus. Thus, ID2 acts primarily through E protein neutralization to segregate T cells and ILCs.
Murre, C. Helix-loop-helix proteins and the advent of cellular diversity: 30 years of discovery. Genes Dev. 33, 6–25 (2019).
Braunstein, M. & Anderson, M. K. HEB in the spotlight: transcriptional regulation of T-cell specification, commitment, and developmental plasticity. Clin. Dev. Immunol. 2012, 678705 (2012).
Bain, G. et al. E2A deficiency leads to abnormalities in αβ T-cell development and to rapid development of T-cell lymphomas. Mol. Cell Biol. 17, 4782–4791 (1997).
Wojciechowski, J., Lai, A., Kondo, M. & Zhuang, Y. E2A and HEB are required to block thymocyte proliferation prior to pre-TCR expression. J. Immunol. 178, 5717–5726 (2007).
Ikawa, T., Kawamoto, H., Goldrath, A. W. & Murre, C. E proteins and notch signaling cooperate to promote T cell lineage specification and commitment. J. Exp. Med. 203, 1329–1342 (2006).
Pereira de Sousa, A. et al. Inhibitors of DNA binding proteins restrict T cell potential by repressing Notch1 expression in Flt3-negative common lymphoid progenitors. J. Immunol. 189, 3822–3830 (2012).
Yashiro-Ohtani, Y. et al. Pre-TCR signaling inactivates Notch1 transcription by antagonizing E2A. Genes Dev. 23, 1665–1676 (2009).
Zook, E. C. & Kee, B. L. Development of innate lymphoid cells. Nat. Immunol. 17, 775–782 (2016).
Moro, K. et al. Innate production of TH2 cytokines by adipose tissue-associated c-Kit+Sca-1+ lymphoid cells. Nature 463, 540–544 (2010).
Koues, O. I. et al. Distinct gene regulatory pathways for human innate versus adaptive lymphoid cells. Cell 165, 1134–1146 (2016).
Boos, M. D., Yokota, Y., Eberl, G. & Kee, B. L. Mature natural killer cell and lymphoid tissue-inducing cell development requires Id2-mediated suppression of E protein activity. J. Exp. Med. 204, 1119–1130 (2007).
Hosokawa, H. et al. Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16. Nat. Immunol. 19, 1427–1440 (2018). This study reveals the molecular basis of both direct and indirect BCL-11B actions to promote T cell identity and to avoid alternative lineage phenotypes in the thymus. Among the BCL-11B-repressed targets, Id2 and Zbtb16 are shown to be functionally important to control distinct alternative programmes.
Ikawa, T., Fujimoto, S., Kawamoto, H., Katsura, Y. & Yokota, Y. Commitment to natural killer cells requires the helix-loop-helix inhibitor Id2. Proc. Natl Acad. Sci. USA 98, 5164–5169 (2001).
Zook, E. C. et al. Transcription factor ID2 prevents E proteins from enforcing a naive T lymphocyte gene program during NK cell development. Sci. Immunol. 3, eaao2139 (2018).
Miyazaki, M. et al. The opposing roles of the transcription factor E2A and its antagonist Id3 that orchestrate and enforce the naive fate of T cells. Nat. Immunol. 12, 992–1001 (2011).
Jones, M. E. & Zhuang, Y. Stage-specific functions of E-proteins at the β-selection and T-cell receptor checkpoints during thymocyte development. Immunol. Res. 49, 202–215 (2011).
Jones, M. E. & Zhuang, Y. Regulation of V(D)J recombination by E-protein transcription factors. Adv. Exp. Med. Biol. 650, 148–156 (2009).
Jones, M. E. & Zhuang, Y. Acquisition of a functional T cell receptor during T lymphocyte development is enforced by HEB and E2A transcription factors. Immunity 27, 860–870 (2007).
Bain, G. et al. Regulation of the helix-loop-helix proteins, E2A and Id3, by the Ras-ERK MAPK cascade. Nat. Immunol. 2, 165–171 (2001).
Jones-Mason, M. E. et al. E protein transcription factors are required for the development of CD4+ lineage T cells. Immunity 36, 348–361 (2012).
Phelan, J. D. et al. Growth factor independent-1 maintains Notch1-dependent transcriptional programming of lymphoid precursors. PLoS Genet. 9, e1003713 (2013).
Emambokus, N. et al. Progression through key stages of haemopoiesis is dependent on distinct threshold levels of c-Myb. EMBO J. 22, 4478–4488 (2003).
Allen, R. D. III, Bender, T. P. & Siu, G. c-Myb is essential for early T cell development. Genes Dev. 13, 1073–1078 (1999).
Georgopoulos, K. The making of a lymphocyte: the choice among disparate cell fates and the IKAROS enigma. Genes Dev. 31, 439–450 (2017).
Ebihara, T., Seo, W. & Taniuchi, I. Roles of RUNX complexes in immune cell development. Adv. Exp. Med. Biol. 962, 395–413 (2017).
Guo, Y., Maillard, I., Chakraborti, S., Rothenberg, E. V. & Speck, N. A. Core binding factors are necessary for natural killer cell development, and cooperate with Notch signaling during T cell specification. Blood 112, 480–492 (2008).
Geimer Le Lay, A. S. et al. The tumor suppressor Ikaros shapes the repertoire of Notch target genes in T cells. Sci. Signal. 7, ra28 (2014).
Winandy, S., Wu, L., Wang, J. H. & Georgopoulos, K. Pre-T cell receptor (TCR) and TCR-controlled checkpoints in T cell differentiation are set by Ikaros. J. Exp. Med. 190, 1039–1048 (1999).
Arenzana, T. L., Schjerven, H. & Smale, S. T. Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor. Genes Dev. 29, 1801–1816 (2015).
Hosokawa, H. et al. Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding. Immunity 48, 1119–1134 e7 (2018). PU.1 directly activates its target genes in part by recruiting RUNX1 and SATB1. The result is to ‘steal’ RUNX1 and SATB1 from sites associated with T cell lineage-related genes, thus repressing some of these genes, indirectly, without direct DNA binding.
David-Fung, E. S. et al. Transcription factor expression dynamics of early T-lymphocyte specification and commitment. Dev. Biol. 325, 444–467 (2009).
Talebian, L. et al. T-lymphoid, megakaryocyte, and granulocyte development are sensitive to decreases in CBFβ dosage. Blood 109, 11–21 (2007).
Cortes, M., Wong, E., Koipally, J. & Georgopoulos, K. Control of lymphocyte development by the Ikaros gene family. Curr. Opin. Biol. 11, 167–171 (1999).
Liu, P., Li, P. & Burke, S. Critical roles of Bcl11b in T-cell development and maintenance of T-cell identity. Immunol. Rev. 238, 138–149 (2010).
Kominami, R. Role of the transcription factor Bcl11b in development and lymphomagenesis. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 88, 72–87 (2012).
Kastner, P. et al. Bcl11b represses a mature T-cell gene expression program in immature CD4+CD8+ thymocytes. Eur. J. Immunol. 40, 2143–2154 (2010).
Li, L., Leid, M. & Rothenberg, E. V. An early T cell lineage commitment checkpoint dependent on the transcription factor Bcl11b. Science 329, 89–93 (2010).
Shibata, K. et al. IFN-γ-producing and IL-17-producing γδ T cells differentiate at distinct developmental stages in murine fetal thymus. J. Immunol. 192, 2210–2218 (2014).
De Obaldia, M. E. & Bhandoola, A. Transcriptional regulation of innate and adaptive lymphocyte lineages. Annu. Rev. Immunol. 33, 607–642 (2015).
Avram, D. & Califano, D. The multifaceted roles of Bcl11b in thymic and peripheral T cells: impact on immune diseases. J. Immunol. 193, 2059–2065 (2014).
Fang, D. et al. Bcl11b, a novel GATA3-interacting protein, suppresses Th1 while limiting Th2 cell differentiation. J. Exp. Med. 215, 1449–1462 (2018).
Punwani, D. et al. Multisystem anomalies in severe combined immunodeficiency with mutant BCL11B. N. Engl. J. Med. 375, 2165–2176 (2016).
Hirose, S. et al. Bcl11b prevents the intrathymic development of innate CD8 T cells in a cell intrinsic manner. Int. Immunol. 27, 205–215 (2015).
Kojo, S. et al. Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes. Nat. Commun. 8, 702 (2017).
Longabaugh, W. J. R. et al. Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc. Natl Acad. Sci. USA 114, 5800–5807 (2017).
Ikawa, T. et al. An essential developmental checkpoint for production of the T cell lineage. Science 329, 93–96 (2010).
Li, P. et al. Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion. Science 329, 85–89 (2010).
Kadoch, C. & Crabtree, G. R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics. Sci. Adv. 1, e1500447 (2015).
Cismasiu, V. B. et al. BCL11B functionally associates with the NuRD complex in T lymphocytes to repress targeted promoter. Oncogene 24, 6753–6764 (2005).
Hosokawa, H. et al. Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells. J. Exp. Med. 217, e20190972 (2020). Bcl11b is expressed in pro-T cells and ILC2s. Id2 is an important repressed target gene of BCL-11B in pro-T cells, whereas Id2 must be co-expressed with Bcl11b in ILC2s. This study show that BCL-11B regulates distinct sets of genes in pro-T cells and ILC2s by organizing distinct protein complexes and binding to different genomic regions.
Ng, K. K. et al. A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment. eLife 7, e37851 (2018). This article shows that cis-acting epigenetic constraints cause delays of the order of days in the activation of Bcl11b for T cell lineage commitment. The authors establish two-colour Bcl11b reporter mice to monitor the activation status and enhancer dependence of Bcl11b alleles separately.
Li, L. et al. A far downstream enhancer for murine Bcl11b controls its T-cell specific expression. Blood 122, 902–911 (2013).
Rothenberg, E. V. Dynamic control of the T-cell specification gene regulatory network. Curr. Opin. Syst. Biol. 18, 62–76 (2019).
Champhekar, A. et al. Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1. Genes Dev. 29, 832–848 (2015).
Rothenberg, E. V., Hosokawa, H. & Ungerback, J. Mechanisms of action of hematopoietic transcription factor PU.1 in initiation of T-cell development. Front. Immunol. 10, 228 (2019).
Kawamoto, H. et al. Extensive proliferation of T cell lineage-restricted progenitors in the thymus: an essential process for clonal expression of diverse T cell receptor β chains. Eur. J. Immunol. 33, 606–615 (2003).
Scott, E. W., Simon, M. C., Anastasi, J. & Singh, H. Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages. Science 265, 1573–1577 (1994).
Kueh, H. Y., Champhekar, A., Nutt, S. L., Elowitz, M. B. & Rothenberg, E. V. Positive feedback between PU.1 and the cell cycle controls myeloid differentiation. Science 341, 670–673 (2013).
Heinz, S. et al. Effect of natural genetic variation on enhancer selection and function. Nature 503, 487–492 (2013).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Ostuni, R. et al. Latent enhancers activated by stimulation in differentiated cells. Cell 152, 157–171 (2013).
Escalante, C. R. et al. Crystal structure of PU.1/IRF-4/DNA ternary complex. Mol. Cell 10, 1097–1105 (2002).
Minderjahn, J. et al. Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat. Commun. 11, 402 (2020).
Carotta, S. et al. The transcription factor PU.1 controls dendritic cell development and Flt3 cytokine receptor expression in a dose-dependent manner. Immunity 32, 628–641 (2010).
Seki, M. et al. Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia. Nat. Genet. 49, 1274–1281 (2017).
Rosenbauer, F. et al. Lymphoid cell growth and transformation are suppressed by a key regulatory element of the gene encoding PU.1. Nat. Genet. 38, 27–37 (2006).
Franco, C. B. et al. Notch/Delta signaling constrains reengineering of pro-T cells by PU.1. Proc. Natl Acad. Sci. USA 103, 11993–11998 (2006).
Laiosa, C. V., Stadtfeld, M., Xie, H., de Andres-Aguayo, L. & Graf, T. Reprogramming of committed T cell progenitors to macrophages and dendritic cells by C/EBPα and PU.1 transcription factors. Immunity 25, 731–744 (2006).
Yu, Y. et al. Bcl11a is essential for lymphoid development and negatively regulates p53. J. Exp. Med. 209, 2467–2483 (2012).
Zohren, F. et al. The transcription factor Lyl-1 regulates lymphoid specification and the maintenance of early T lineage progenitors. Nat. Immunol. 13, 761–769 (2012).
Yui, M. A., Feng, N. & Rothenberg, E. V. Fine-scale staging of T cell lineage commitment in adult mouse thymus. J. Immunol. 185, 284–293 (2010).
Masuda, K. et al. T cell lineage determination precedes the initiation of TCR β gene rearrangement. J. Immunol. 179, 3699–3706 (2007).
Bell, J. J. & Bhandoola, A. The earliest thymic progenitors for T cells possess myeloid lineage potential. Nature 452, 764–767 (2008).
Wada, H. et al. Adult T-cell progenitors retain myeloid potential. Nature 452, 768–772 (2008).
De Obaldia, M. E., Bell, J. J. & Bhandoola, A. Early T-cell progenitors are the major granulocyte precursors in the adult mouse thymus. Blood 121, 64–71 (2013).
Zarnegar, M. A., Chen, J. & Rothenberg, E. V. Cell-type-specific activation and repression of PU.1 by a complex of discrete, functionally specialized cis-regulatory elements. Mol. Cell. Biol. 30, 4922–4939 (2010).
Huang, G. et al. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis. Nat. Genet. 40, 51–60 (2008).
Kueh, H. Y. et al. Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment. Nat. Immunol. 17, 956–965 (2016).
Rothenberg, E. V. Programming for T-lymphocyte fates: modularity and mechanisms. Genes Dev. 33, 1117–1135 (2019).
Isoda, T. et al. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate. Cell 171, 103–119 e18 (2017). The authors focus on the distal superenhancer region of Bcl11b and show that it harbours a functionally important long non-coding RNA that acts positively on gene regulation. The authors find a severe, allele-specific loss of Bcl11b expression when long non-coding RNA transcription is truncated.
Manesso, E., Chickarmane, V., Kueh, H. Y., Rothenberg, E. V. & Peterson, C. Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence. J. R. Soc. Interface 10, 20120774 (2013).
Krueger, A., Ziętara, N. & Łyszkiewicz, M. T cell development by the numbers. Trends Immunol. 38, 128–139 (2017).
Cumano, A. et al. New molecular insights into immune cell development. Annu. Rev. Immunol. 37, 497–519 (2019).
Casero, D. et al. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages. Nat. Immunol. 16, 1282–1291 (2015).
Ha, V. L. et al. The T-ALL related gene BCL11B regulates the initial stages of human T-cell differentiation. Leukemia 31, 2503–2514 (2017).
Canté-Barrett, K. et al. Loss of CD44dim expression from early progenitor cells marks T-cell lineage commitment in the human thymus. Front. Immunol. 8, 32 (2017).
Garvie, C. W., Pufall, M. A., Graves, B. J. & Wolberger, C. Structural analysis of the autoinhibition of Ets-1 and its role in protein partnerships. J. Biol. Chem. 277, 45529–45536 (2002).
Pufall, M. A. & Graves, B. J. Ets-1 flips for new partner Pax-5. Structure 10, 11–14 (2002).
Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994–1004 (2012).
Iwafuchi-Doi, M. & Zaret, K. S. Cell fate control by pioneer transcription factors. Development 143, 1833–1837 (2016).
Chronis, C. et al. Cooperative binding of transcription factors orchestrates reprogramming. Cell 168, 442–459 (2017).
Weikum, E. R., Knuesel, M. T., Ortlund, E. A. & Yamamoto, K. R. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat. Rev. Mol. Cell. Biol. 18, 159–174 (2017).
Luna-Zurita, L. et al. Complex interdependence regulates heterotypic transcription factor distribution and coordinates cardiogenesis. Cell 164, 999–1014 (2016).
Zhang, J. et al. Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis. Nat. Immunol. 13, 86–94 (2011).
Kanhere, A. et al. T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements. Nat. Commun. 3, 1268 (2012).
Garcia-Perez, L. et al. Functional definition of a transcription factor hierarchy regulating T cell lineage commitment. Sci. Adv. 6, eaaw7313 (2020).
The authors thank M. Romero-Wolf for helpful discussions and suggestions, and J. Ungerbäck, X. Wang, M. A. Yui and present and former members of the Rothenberg group, whose helpful discussion and published and unpublished data were important for the ideas in this Review. The authors apologize to colleagues whose relevant work could not be cited owing to space constraints. The authors gratefully acknowledge support from the Japan Society for the Promotion of Science KAKENHI (grant number JP19H03692), the Mochida Memorial Foundation for Medical and Pharmaceutical Research, the Naito Foundation and the Takeda Science Foundation (to H.H.), and from the US Public Health Service (R01AI135200, R01HL119102, R01HD100039 and R01HD076915) and the Albert Billings Ruddock Professorship (to E.V.R).
The authors declare no competing interests.
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- Notch pathway
Notch designates a cell-surface receptor (NOTCH1–NOTCH4 family in mammals) that interacts with cell-bound ligands of the Delta (Delta-like in mammals) and Serrate (Jagged in mammals) families. Originally discovered through its potent role in fruit fly development, Notch signalling controls important embryological switch points for the generation of various cell types in organisms of all kinds.
- Positive selection
Once immature thymocytes at the double-positive stage have expressed a complete T cell receptor-αβ (TCRαβ) complex, the cells are doomed to die unless that TCR can interact with cell-surface molecules on thymic epithelial cells. Positive selection is the TCR-dependent rescue of the cells from death and the choice of helper or killer fate that results from that rescue.
- Negative selection
If the newly expressed T cell receptor (TCR) on double-positive and immature single-positive thymocytes interacts too strongly with surface molecules on thymic antigen-presenting cells, the thymocytes are induced to commit suicide rather than enabled to survive and mature. Negative selection designates this TCR stimulation-dependent suicide.
The first step of T cell development that depends on a form of the T cell receptor (TCR), in this case a special immature form of the TCR consisting of only a TCRβ chain plus an invariant pre-TCRα surrogate chain. This complex is generated when double-negative 3a (DN3a) thymocytes successfully rearrange the genes encoding the TCRβ chain, and its assembly is required to enable the cells to proliferate and differentiate further to become double-positive thymocytes.
- WNT signalling
The WNT pathway is a multistep developmental signalling pathway, often involved in self-renewal of tissue stem cells and in embryonic pattern formation in many organisms. In mammals, a soluble ligand from the large WNT family binds to a cell-surface receptor (of the FZD family), which enables β-catenin to avoid degradation in the cytoplasm and translocate to the nucleus, where it becomes a co-activator for transcription factors of the TCF/LEF family.
- SWI/SNF complex
A nucleosome remodelling protein complex in eukaryotic cells that generally opens chromatin to allow greater transcription factor access. This is thought to be an important step involved in transcriptional activation of many genes.
- Nucleosome remodelling deacetylase complex
(NuRD complex). A nucleosome remodelling protein complex that is recruited by many transcription factors and is often involved in target gene repression. Although the histone deacetylase activity of the complex is often used for repression, the complex as a whole can be involved in various transcriptional regulatory activities.
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Hosokawa, H., Rothenberg, E.V. How transcription factors drive choice of the T cell fate. Nat Rev Immunol (2020). https://doi.org/10.1038/s41577-020-00426-6