Transcription Factor Networks Directing the Development, Function, and Evolution of Innate Lymphoid Effectors

Literature Cited

1. Spits H, Di Santo JP. 1.  2011. The expanding family of innate lymphoid cells: regulators and effectors of immunity and tissue remodeling. Nat. Immunol. 12:21–27 [Google Scholar]
2. Sumaria N, Roediger B, Ng LG, Qin J, Pinto R. 2.  et al. 2011. Cutaneous immunosurveillance by self-renewing dermal γΔ T cells. J. Exp. Med. 208:505–18 [Google Scholar]
3. Kastenmuller W, Torabi-Parizi P, Subramanian N, Lammermann T, Germain RN. 3.  2012. A spatially-organized multicellular innate immune response in lymph nodes limits systemic pathogen spread. Cell 150:1235–48 [Google Scholar]
4. Sheridan BS, Lefrançois L. 4.  2011. Regional and mucosal memory T cells. Nat. Immunol. 12:485–91 [Google Scholar]
5. Mueller SN, Gebhardt T, Carbone FR, Heath WR. 5.  2013. Memory T cell subsets, migration patterns, and tissue residence. Annu. Rev. Immunol. 31:137–61 [Google Scholar]
6. Mosmann TR, Cherwinski H, Bond MW, Giedlin MA, Coffman RL. 6.  1986. Two types of murine helper T cell clones. I. Definition according to profiles of lymphokine activities and secreted protein. J. Immunol. 136:2348–57 [Google Scholar]
7. Harrington LE, Hatton RD, Mangan PR, Turner H, Murphy TL. 7.  et al. 2005. Interleukin 17-producing CD4⁺ effector T cells develop via a lineage distinct from the T helper type 1 and 2 lineages. Nat. Immunol. 6:1123–32 [Google Scholar]
8. Park H, Li Z, Yang XO, Chang SH, Nurieva R. 8.  et al. 2005. A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat. Immunol. 6:1133–41 [Google Scholar]
9. Zheng W, Flavell RA. 9.  1997. The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 89:587–96 [Google Scholar]
10. Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG, Glimcher LH. 10.  2000. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100:655–69 [Google Scholar]
11. Ivanov II, McKenzie BS, Zhou L, Tadokoro CE, Lepelley A. 11.  et al. 2006. The orphan nuclear receptor RORγt directs the differentiation program of proinflammatory IL-17⁺ T helper cells. Cell 126:1121–33 [Google Scholar]
12. Yang XO, Pappu BP, Nurieva R, Akimzhanov A, Kang HS. 12.  et al. 2008. T helper 17 lineage differentiation is programmed by orphan nuclear receptors ROR alpha and ROR gamma. Immunity 28:29–39 [Google Scholar]
13. Kang SJ, Liang HE, Reizis B, Locksley RM. 13.  2008. Regulation of hierarchical clustering and activation of innate immune cells by dendritic cells. Immunity 29:819–33 [Google Scholar]
14. Laird DJ, De Tomaso AW, Cooper MD, Weissman IL. 14.  2000. 50 million years of chordate evolution: seeking the origins of adaptive immunity. PNAS 97:6924–26 [Google Scholar]
15. Boehm T, McCurley N, Sutoh Y, Schorpp M, Kasahara M, Cooper MD. 15.  2012. VLR-based adaptive immunity. Annu. Rev. Immunol. 30:203–20 [Google Scholar]
16. Spits H, Artis D, Colonna M, Diefenbach A, Di Santo JP. 16.  et al. 2013. Innate lymphoid cells—a proposal for uniform nomenclature. Nat. Rev. Immunol. 13:145–49 [Google Scholar]
17. Montecino-Rodriguez E, Dorshkind K. 17.  2012. B-1 B cell development in the fetus and adult. Immunity 36:13–21 [Google Scholar]
18. Bonneville M, O'Brien RL, Born WK. 18.  2010. γΔ T cell effector functions: a blend of innate programming and acquired plasticity. Nat. Rev. Immunol. 10:467–78 [Google Scholar]
19. Chen L, He W, Kim ST, Tao J, Gao Y. 19.  et al. 2007. Epigenetic and transcriptional programs lead to default IFN-γ production by γΔ T cells. J. Immunol. 178:2730–36 [Google Scholar]
20. Vosshenrich CA, Di Santo JP. 20.  2013. Developmental programming of natural killer and innate lymphoid cells. Curr. Opin. Immunol. 25:130–38 [Google Scholar]
21. Jameson J, Havran WL. 21.  2007. Skin γΔ T-cell functions in homeostasis and wound healing. Immunol. Rev. 215:114–22 [Google Scholar]
22. Garman RD, Doherty PJ, Raulet DH. 22.  1986. Diversity, rearrangement and expression of murine T cell gamma genes. Cell 45:733–42 [Google Scholar]
23. Shires J, Theodoridis E, Hayday AC. 23.  2001. Biological insights into TCRγΔ⁺ and TCRαβ⁺ intraepithelial lymphocytes provided by serial analysis of gene expression (SAGE). Immunity 15:419–34 [Google Scholar]
24. Ismail AS, Behrendt CL, Hooper LV. 24.  2009. Reciprocal interactions between commensal bacteria and gamma delta intraepithelial lymphocytes during mucosal injury. J. Immunol. 182:3047–54 [Google Scholar]
25. Li Y, Innocentin S, Withers DR, Roberts NA, Gallagher AR. 25.  et al. 2011. Exogenous stimuli maintain intraepithelial lymphocytes via aryl hydrocarbon receptor activation. Cell 147:629–40 [Google Scholar]
26. Shui JW, Larange A, Kim G, Vela JL, Zahner S. 26.  et al. 2012. HVEM signalling at mucosal barriers provides host defence against pathogenic bacteria. Nature 488:222–25 [Google Scholar]
27. Grigoriadou K, Boucontet L, Pereira P. 27.  2003. Most IL-4-producing gamma delta thymocytes of adult mice originate from fetal precursors. J. Immunol. 171:2413–20 [Google Scholar]
28. Stark MA, Huo Y, Burcin TL, Morris MA, Olson TS, Ley K. 28.  2005. Phagocytosis of apoptotic neutrophils regulates granulopoiesis via IL-23 and IL-17. Immunity 22:285–94 [Google Scholar]
29. Lockhart E, Green AM, Flynn JL. 29.  2006. IL-17 production is dominated by γΔ T cells rather than CD4 T cells during Mycobacterium tuberculosis infection. J. Immunol. 177:4662–69 [Google Scholar]
30. Azuara V, Levraud JP, Lembezat MP, Pereira P. 30.  1997. A novel subset of adult gamma delta thymocytes that secretes a distinct pattern of cytokines and expresses a very restricted T cell receptor repertoire. Eur. J. Immunol. 27:544–53 [Google Scholar]
31. Lee YJ, Jameson SC, Hogquist KA. 31.  2011. Alternative memory in the CD8 T cell lineage. Trends Immunol. 32:50–56 [Google Scholar]
32. Narayan K, Sylvia KE, Malhotra N, Yin CC, Martens G. 32.  et al. 2012. Intrathymic programming of effector fates in three molecularly distinct γΔ T cell subtypes. Nat. Immunol. 13:511–18 [Google Scholar]
33. Matsuzaki G, Hiromatsu K, Yoshikai Y, Muramori K, Nomoto K. 33.  1993. Characterization of T-cell receptor gamma delta T cells appearing at the early phase of murine Listeria monocytogenes infection. Immunology 78:22–27 [Google Scholar]
34. Mombaerts P, Arnoldi J, Russ F, Tonegawa S, Kaufmann S. 34.  1993. Different roles of αβ and γΔ T cells in immunity against an intracellular bacterial pathogen. Nature 365:53–56 [Google Scholar]
35. Cai Y, Shen X, Ding C, Qi C, Li K. 35.  et al. 2011. Pivotal role of dermal IL-17-producing γΔ T cells in skin inflammation. Immunity 35:596–610 [Google Scholar]
36. Malhotra N, Narayan K, Cho OH, Sylvia KE, Yin C. 36.  et al. 2013. A network of high-mobility group box transcription factors programs innate interleukin-17 production. Immunity 38:681–93 [Google Scholar]
37. Gray EE, Ramirez-Valle F, Xu Y, Wu S, Wu Z. 37.  et al. 2013. Deficiency in IL-17-committed Vγ4⁺ γΔ T cells in a spontaneous Sox13-mutant CD45.1⁺ congenic mouse substrain provides protection from dermatitis. Nat. Immunol. 14:584–92 [Google Scholar]
38. Sheridan BS, Romagnoli PA, Pham QM, Fu HH, Alonzo F 3rd. 38.  et al. 2013. γΔ T cells exhibit multifunctional and protective memory in intestinal tissues. Immunity 39:184–95 [Google Scholar]
39. Sun JC, Ugolini S, Vivier E. 39.  2014. Immunological memory within the innate immune system. EMBO J. 33:1295–303 [Google Scholar]
40. Simonian PL, Wehrmann F, Roark CL, Born WK, O'Brien RL, Fontenot AP. 40.  2010. γΔ T cells protect against lung fibrosis via IL-22. J. Exp. Med. 207:2239–53 [Google Scholar]
41. Mielke LA, Jones SA, Raverdeau M, Higgs R, Stefanska A. 41.  et al. 2013. Retinoic acid expression associates with enhanced IL-22 production by γΔ T cells and innate lymphoid cells and attenuation of intestinal inflammation. J. Exp. Med. 210:1117–24 [Google Scholar]
42. van de Pavert SA, Ferreira M, Domingues RG, Ribeiro H, Molenaar R. 42.  et al. 2014. Maternal retinoids control type 3 innate lymphoid cells and set the offspring immunity. Nature 508:123–27 [Google Scholar]
43. Jensen KD, Su X, Shin S, Li L, Youssef S. 43.  et al. 2008. Thymic selection determines γΔ T cell effector fate: Antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon γ. Immunity 29:90–100 [Google Scholar]
44. Ribot JC, deBarros A, Pang DJ, Neves JF, Peperzak V. 44.  et al. 2009. CD27 is a thymic determinant of the balance between interferon-γ- and interleukin 17-producing γΔ T cell subsets. Nat. Immunol. 10:427–36 [Google Scholar]
45. Shay T, Kang J. 45.  2013. Immunological Genome Project and systems immunology. Trends Immunol. 34:602–9 [Google Scholar]
46. Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R. 46.  et al. 2013. The transcriptional landscape of αβ T cell differentiation. Nat. Immunol. 14:619–32 [Google Scholar]
47. Bendelac A, Schwartz RH. 47.  1991. CD4⁺ and CD8⁺ T cells acquire specific lymphokine secretion potentials during thymic maturation. Nature 353:68–71 [Google Scholar]
48. Makino Y, Kanno R, Ito T, Higashino K, Taniguchi M. 48.  1995. Predominant expression of invariant Vα14⁺ TCR α chain in NK1.1⁺ T cell populations. Int. Immunol. 7:1157–61 [Google Scholar]
49. Bendelac A, Lantz O, Quimby ME, Yewdell JW, Bennink JR, Brutkiewicz RR. 49.  1995. CD1 recognition by mouse NK1⁺ T lymphocytes. Science 268:863–65 [Google Scholar]
50. Kawano T, Cui J, Koezuka Y, Toura I, Kaneko Y. 50.  et al. 1997. CD1d-restricted and TCR-mediated activation of Vα14 NKT cells by glycosylceramides. Science 278:1626–29 [Google Scholar]
51. Savage AK, Constantinides MG, Han J, Picard D, Martin E. 51.  et al. 2008. The transcription factor PLZF directs the effector program of the NKT cell lineage. Immunity 29:391–403 [Google Scholar]
52. Kovalovsky D, Uche OU, Eladad S, Hobbs RM, Yi W. 52.  et al. 2008. The BTB-zinc finger transcriptional regulator PLZF controls the development of invariant natural killer T cell effector functions. Nat. Immunol. 9:1055–64 [Google Scholar]
53. Doulatov S, Notta F, Rice KL, Howell L, Zelent A. 53.  et al. 2009. PLZF is a regulator of homeostatic and cytokine-induced myeloid development. Genes Dev. 23:2076–87 [Google Scholar]
54. Cohen NR, Brennan PJ, Shay T, Watts GF, Brigl M. 54.  et al. 2013. Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nat. Immunol. 14:90–99 [Google Scholar]
55. Godfrey DI, Stankovic S, Baxter AG. 55.  2010. Raising the NKT cell family. Nat. Immunol. 11:197–206 [Google Scholar]
56. Lee YJ, Holzapfel KL, Zhu J, Jameson SC, Hogquist KA. 56.  2013. Steady-state production of IL-4 modulates immunity in mouse strains and is determined by lineage diversity of iNKT cells. Nat. Immunol. 14:1146–54 [Google Scholar]
57. Benlagha K, Kyin T, Beavis A, Teyton L, Bendelac A. 57.  2002. A thymic precursor to the NK T cell lineage. Science 296:553–55 [Google Scholar]
58. Treiner E, Duban L, Bahram S, Radosavljevic M, Wanner V. 58.  et al. 2003. Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1. Nature 422:164–69 [Google Scholar]
59. Kjer-Nielsen L, Patel O, Corbett AJ, Le Nours J, Meehan B. 59.  et al. 2012. MR1 presents microbial vitamin B metabolites to MAIT cells. Nature 491:717–23 [Google Scholar]
60. Le Bourhis L, Martin E, Peguillet I, Guihot A, Froux N. 60.  et al. 2010. Antimicrobial activity of mucosal-associated invariant T cells. Nat. Immunol. 11:701–8 [Google Scholar]
61. Dusseaux M, Martin E, Serriari N, Peguillet I, Premel V. 61.  et al. 2011. Human MAIT cells are xenobiotic-resistant, tissue-targeted, CD161^hi IL-17–secreting T cells. Blood 117:1250–59 [Google Scholar]
62. Meierovics A, Yankelevich WJ, Cowley SC. 62.  2013. MAIT cells are critical for optimal mucosal immune responses during in vivo pulmonary bacterial infection. PNAS 110:E3119–28 [Google Scholar]
63. Leeansyah E, Loh L, Nixon DF, Sandberg JK. 63.  2014. Acquisition of innate-like microbial reactivity in mucosal tissues during human fetal MAIT-cell development. Nat. Commun. 5:3143 [Google Scholar]
64. Van Rhijn I, Kasmar A, de Jong A, Gras S, Bhati M. 64.  et al. 2013. A conserved human T cell population targets mycobacterial antigens presented by CD1b. Nat. Immunol. 14:706–13 [Google Scholar]
65. Beagley KW, Fujihashi K, Lagoo AS, Lagoo-Deenadaylan S, Black CA. 65.  et al. 1995. Differences in intraepithelial lymphocyte T cell subsets isolated from murine small versus large intestine. J. Immunol. 154:5611–19 [Google Scholar]
66. Yamagata T, Mathis D, Benoist C. 66.  2004. Self-reactivity in thymic double-positive cells commits cells to a CD8αα lineage with characteristics of innate immune cells. Nat. Immunol. 5:597–605 [Google Scholar]
67. Konkel JE, Maruyama T, Carpenter AC, Xiong Y, Zamarron BF. 67.  et al. 2011. Control of the development of CD8αα⁺ intestinal intraepithelial lymphocytes by TGF-β. Nat. Immunol. 12:312–19 [Google Scholar]
68. Leishman AJ, Naidenko OV, Attinger A, Koning F, Lena CJ. 68.  et al. 2001. T cell responses modulated through interaction between CD8αα and the nonclassical MHC class I molecule, TL. Science 294:1936–39 [Google Scholar]
69. Rutz S, Eidenschenk C, Ouyang W. 69.  2013. IL-22, not simply a Th17 cytokine. Immunol. Rev. 252:116–32 [Google Scholar]
70. Li W, Sofi MH, Yeh N, Sehra S, McCarthy BP. 70.  et al. 2007. Thymic selection pathway regulates the effector function of CD4 T cells. J. Exp. Med. 204:2145–57 [Google Scholar]
71. Marks BR, Nowyhed HN, Choi JY, Poholek AC, Odegard JM. 71.  et al. 2009. Thymic self-reactivity selects natural interleukin 17-producing T cells that can regulate peripheral inflammation. Nat. Immunol. 10:1125–32 [Google Scholar]
72. Prince AL, Watkin LB, Yin CC, Selin LK, Kang J. 72.  et al. 2014. Innate PLZF⁺CD4⁺ αβ T cells develop and expand in the absence of Itk. J. Immunol. 193:673–87 [Google Scholar]
73. Rodgers JR, Cook RG. 73.  2005. MHC class Ib molecules bridge innate and acquired immunity. Nat. Rev. Immunol. 5:459–71 [Google Scholar]
74. Bix M, Coles M, Raulet D. 74.  1993. Positive selection of Vβ8⁺CD4⁻CD8⁻ thymocytes by class I molecules expressed by hematopoietic cells. J. Exp. Med. 178:901–8 [Google Scholar]
75. Li J, Wu D, Jiang N, Zhuang Y. 75.  2013. Combined deletion of Id2 and Id3 genes reveals multiple roles for E proteins in invariant NKT cell development and expansion. J. Immunol. 191:5052–64 [Google Scholar]
76. Verykokakis M, Krishnamoorthy V, Iavarone A, Lasorella A, Sigvardsson M, Kee BL. 76.  2013. Essential functions for ID proteins at multiple checkpoints in invariant NKT cell development. J. Immunol. 191:5973–83 [Google Scholar]
77. Satoh-Takayama N, Vosshenrich CA, Lesjean-Pottier S, Sawa S, Lochner M. 77.  et al. 2008. Microbial flora drives interleukin 22 production in intestinal NKp46⁺ cells that provide innate mucosal immune defense. Immunity 29:958–70 [Google Scholar]
78. Sanos SL, Bui VL, Mortha A, Oberle K, Heners C. 78.  et al. 2009. RORγt and commensal microflora are required for the differentiation of mucosal interleukin 22-producing NKp46⁺ cells. Nat. Immunol. 10:83–91 [Google Scholar]
79. Luci C, Reynders A, Ivanov II, Cognet C, Chiche L. 79.  et al. 2009. Influence of the transcription factor RORγt on the development of NKp46⁺ cell populations in gut and skin. Nat. Immunol. 10:75–82 [Google Scholar]
80. Moro K, Yamada T, Tanabe M, Takeuchi T, Ikawa T. 80.  et al. 2010. Innate production of T_H2 cytokines by adipose tissue-associated c-Kit⁺Sca-1⁺ lymphoid cells. Nature 463:540–44 [Google Scholar]
81. Neill DR, Wong SH, Bellosi A, Flynn RJ, Daly M. 81.  et al. 2010. Nuocytes represent a new innate effector leukocyte that mediates type-2 immunity. Nature 464:1367–70 [Google Scholar]
82. Cherrier M, Eberl G. 82.  2012. The development of LTi cells. Curr. Opin. Immunol. 24:178–83 [Google Scholar]
83. Bernink JH, Peters CP, Munneke M, te Velde AA, Meijer SL. 83.  et al. 2013. Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues. Nat. Immunol. 14:221–29 [Google Scholar]
84. Fuchs A, Vermi W, Lee JS, Lonardi S, Gilfillan S. 84.  et al. 2013. Intraepithelial type 1 innate lymphoid cells are a unique subset of IL-12- and IL-15-responsive IFN-gamma-producing cells. Immunity 38:769–81 [Google Scholar]
85. Klose CS, Flach M, Mohle L, Rogell L, Hoyler T. 85.  et al. 2014. Differentiation of type 1 ILCs from a common progenitor to all helper-like innate lymphoid cell lineages. Cell 157:340–56 [Google Scholar]
86. Nussbaum JC, Van Dyken SJ, von Moltke J, Cheng LE, Mohapatra A. 86.  et al. 2013. Type 2 innate lymphoid cells control eosinophil homeostasis. Nature 502:245–48 [Google Scholar]
87. Sonnenberg GF, Monticelli LA, Elloso MM, Fouser LA, Artis D. 87.  2011. CD4⁺ lymphoid tissue-inducer cells promote innate immunity in the gut. Immunity 34:122–34 [Google Scholar]
88. Sawa S, Cherrier M, Lochner M, Satoh-Takayama N, Fehling HJ. 88.  et al. 2010. Lineage relationship analysis of RORγt⁺ innate lymphoid cells. Science 330:665–69 [Google Scholar]
89. Kruglov AA, Grivennikov SI, Kuprash DV, Winsauer C, Prepens S. 89.  et al. 2013. Nonredundant function of soluble LTα3 produced by innate lymphoid cells in intestinal homeostasis. Science 342:1243–46 [Google Scholar]
90. Takatori H, Kanno Y, Watford WT, Tato CM, Weiss G. 90.  et al. 2009. Lymphoid tissue inducer-like cells are an innate source of IL-17 and IL-22. J. Exp. Med. 206:35–41 [Google Scholar]
91. Klose CS, Kiss EA, Schwierzeck V, Ebert K, Hoyler T. 91.  et al. 2013. A T-bet gradient controls the fate and function of CCR6-RORγt⁺ innate lymphoid cells. Nature 494:261–65 [Google Scholar]
92. Rankin LC, Groom JR, Chopin M, Herold MJ, Walker JA. 92.  et al. 2013. The transcription factor T-bet is essential for the development of NKp46⁺ innate lymphocytes via the Notch pathway. Nat. Immunol. 14:389–95 [Google Scholar]
93. Ghoreschi K, Laurence A, Yang XP, Tato CM, McGeachy MJ. 93.  et al. 2010. Generation of pathogenic T_H17 cells in the absence of TGF-beta signalling. Nature 467:967–71 [Google Scholar]
94. Townsend MJ, Weinmann AS, Matsuda JL, Salomon R, Farnham PJ. 94.  et al. 2004. T-bet regulates the terminal maturation and homeostasis of NK and Vα14i NKT cells. Immunity 20:477–94 [Google Scholar]
95. Gordon SM, Chaix J, Rupp LJ, Wu J, Madera S. 95.  et al. 2012. The transcription factors T-bet and Eomes control key checkpoints of natural killer cell maturation. Immunity 36:55–67 [Google Scholar]
96. Lazarevic V, Glimcher LH, Lord GM. 96.  2013. T-bet: a bridge between innate and adaptive immunity. Nat. Rev. Immunol. 13:777–89 [Google Scholar]
97. Daussy C, Faure F, Mayol K, Viel S, Gasteiger G. 97.  et al. 2014. T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow. J. Exp. Med. 211:563–77 [Google Scholar]
98. Mjosberg J, Bernink J, Golebski K, Karrich JJ, Peters CP. 98.  et al. 2012. The transcription factor GATA3 is essential for the function of human type 2 innate lymphoid cells. Immunity 37:649–59 [Google Scholar]
99. Hoyler T, Klose CS, Souabni A, Turqueti-Neves A, Pfeifer D. 99.  et al. 2012. The transcription factor GATA-3 controls cell fate and maintenance of type 2 innate lymphoid cells. Immunity 37:634–48 [Google Scholar]
100. Yagi R, Zhong C, Northrup DL, Yu F, Bouladoux N. 100.  et al. 2014. The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells. Immunity 40:378–88 [Google Scholar]
101. Wong SH, Walker JA, Jolin HE, Drynan LF, Hams E. 101.  et al. 2012. Transcription factor RORα is critical for nuocyte development. Nat. Immunol. 13:229–36 [Google Scholar]
102. Halim TY, MacLaren A, Romanish MT, Gold MJ, McNagny KM, Takei F. 102.  2012. Retinoic-acid-receptor-related orphan nuclear receptor alpha is required for natural helper cell development and allergic inflammation. Immunity 37:463–74 [Google Scholar]
103. Constantinides MG, McDonald BD, Verhoef PA, Bendelac A. 103.  2014. A committed precursor to innate lymphoid cells. Nature 508:397–401 [Google Scholar]
104. Constantinides MG, Bendelac A. 104.  2013. Transcriptional regulation of the NKT cell lineage. Curr. Opin. Immunol. 25:161–67 [Google Scholar]
105. Segal E, Shapira M, Regev A, Pe'er D, Botstein D. 105.  et al. 2003. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34:166–76 [Google Scholar]
106. Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN. 106.  et al. 2011. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144:296–309 [Google Scholar]
107. Yosef N, Regev A. 107.  2011. Impulse control: temporal dynamics in gene transcription. Cell 144:886–96 [Google Scholar]
108. Laurenti E, Doulatov S, Zandi S, Plumb I, Chen J. 108.  et al. 2013. The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment. Nat. Immunol. 14:756–63 [Google Scholar]
109. Hu G, Chen J. 109.  2013. A genome-wide regulatory network identifies key transcription factors for memory CD8⁺ T-cell development. Nat. Commun. 4:2830 [Google Scholar]
110. Jojic V, Shay T, Sylvia K, Zuk O, Sun X. 110.  et al. 2013. Identification of transcriptional regulators in the mouse immune system. Nat. Immunol. 14:633–43 [Google Scholar]
111. Ciofani M, Madar A, Galan C, Sellars M, Mace K. 111.  et al. 2012. A validated regulatory network for Th17 cell specification. Cell 151:289–303 [Google Scholar]
112. Rothenberg EV. 112.  2014. The chromatin landscape and transcription factors in T cell programming. Trends Immunol. 35:195–204 [Google Scholar]
113. Yui MA, Rothenberg EV. 113.  2014. Developmental gene networks: a triathlon on the course to T cell identity. Nat. Rev. Immunol. 14:529–45 [Google Scholar]
114. Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y. 114.  et al. 2013. Dynamic regulatory network controlling T_H17 cell differentiation. Nature 496:461–68 [Google Scholar]
115. De Obaldia ME, Bhandoola A. 115.  2015. Transcriptional regulation of innate and adaptive lymphocyte lineages. Annu. Rev. Immunol. 33:607–42 [Google Scholar]
116. Washburn T, Schweighoffer E, Gridley T, Chang D, Fowlkes BJ. 116.  et al. 1997. Notch activity influences the αβ versus γΔ T cell lineage decision. Cell 88:833–43 [Google Scholar]
117. Massari ME, Murre C. 117.  2000. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 20:429–40 [Google Scholar]
118. Maillard I, Fang T, Pear WS. 118.  2005. Regulation of lymphoid development, differentiation, and function by the Notch pathway. Annu. Rev. Immunol. 23:945–74 [Google Scholar]
119. Rothenberg EV, Moore JE, Yui MA. 119.  2008. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 8:9–21 [Google Scholar]
120. de Pooter RF, Kee BL. 120.  2010. E proteins and the regulation of early lymphocyte development. Immunol. Rev. 238:93–109 [Google Scholar]
121. Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. 121.  2012. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 149:467–82 [Google Scholar]
122. Weber BN, Chi AW, Chavez A, Yashiro-Ohtani Y, Yang Q. 122.  et al. 2011. A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476:63–68 [Google Scholar]
123. Germar K, Dose M, Konstantinou T, Zhang J, Wang H. 123.  et al. 2011. T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. PNAS 108:20060–65 [Google Scholar]
124. Dose M, Emmanuel AO, Chaumeil J, Zhang J, Sun T. 124.  et al. 2014. β-Catenin induces T-cell transformation by promoting genomic instability. PNAS 111:391–96 [Google Scholar]
125. Yokota Y, Mansouri A, Mori S, Sugawara S, Adachi S. 125.  et al. 1999. Development of peripheral lymphoid organs and natural killer cells depends on the helix-loop-helix inhibitor Id2. Nature 397:702–6 [Google Scholar]
126. Cherrier M, Sawa S, Eberl G. 126.  2012. Notch, Id2, and RORγt sequentially orchestrate the fetal development of lymphoid tissue inducer cells. J. Exp. Med. 209:729–40 [Google Scholar]
127. Ikawa T, Kawamoto H, Goldrath AW, Murre C. 127.  2006. E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment. J. Exp. Med. 203:1329–42 [Google Scholar]
128. Verbeek S, Izon D, Hofhuis F, Robanus-Maandag E, te Riele H. 128.  et al. 1995. An HMG-box-containing T-cell factor required for thymocyte differentiation. Nature 374:70–74 [Google Scholar]
129. Clevers H. 129.  2006. Wnt/β-catenin signaling in development and disease. Cell 127:469–80 [Google Scholar]
130. Giese K, Cox J, Grosschedl R. 130.  1992. The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures. Cell 69:185–95 [Google Scholar]
131. Li L, Zhang JA, Dose M, Kueh HY, Mosadeghi R. 131.  et al. 2013. A far downstream enhancer for murine Bcl11b controls its T-cell specific expression. Blood 122:902–11 [Google Scholar]
132. Jogi A, Persson P, Grynfeld A, Pahlman S, Axelson H. 132.  2002. Modulation of basic helix-loop-helix transcription complex formation by Id proteins during neuronal differentiation. J. Biol. Chem. 277:9118–26 [Google Scholar]
133. Li L, Leid M, Rothenberg EV. 133.  2010. An early T cell lineage commitment checkpoint dependent on the transcription factor Bcl11b. Science 329:89–93 [Google Scholar]
134. Li P, Burke S, Wang J, Chen X, Ortiz M. 134.  et al. 2010. Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion. Science 329:85–89 [Google Scholar]
135. Garcia-Ojeda ME, Klein Wolterink RGJ, Lemaitre F, Richard-Le Goff O, Hasan M. 135.  et al. 2013. GATA-3 promotes T-cell specification by repressing B-cell potential in pro-T cells in mice. Blood 121:1749–59 [Google Scholar]
136. Yucel R, Karsunky H, Klein-Hitpass L, Moroy T. 136.  2003. The transcriptional repressor Gfi1 affects development of early, uncommitted c-Kit⁺ T cell progenitors and CD4/CD8 lineage decision in the thymus. J. Exp. Med. 197:831–44 [Google Scholar]
137. Li H, Ji M, Klarmann KD, Keller JR. 137.  2010. Repression of Id2 expression by Gfi-1 is required for B-cell and myeloid development. Blood 116:1060–69 [Google Scholar]
138. Yu S, Zhou X, Steinke FC, Liu C, Chen SC. 138.  et al. 2012. The TCF-1 and LEF-1 transcription factors have cooperative and opposing roles in T cell development and malignancy. Immunity 37:813–26 [Google Scholar]
139. Satoh-Takayama N, Lesjean-Pottier S, Vieira P, Sawa S, Eberl G. 139.  et al. 2010. IL-7 and IL-15 independently program the differentiation of intestinal CD3-NKp46⁺ cell subsets from Id2-dependent precursors. J. Exp. Med. 207:273–80 [Google Scholar]
140. Yang Q, Monticelli LA, Saenz SA, Chi AW, Sonnenberg GF. 140.  et al. 2013. T cell factor 1 is required for group 2 innate lymphoid cell generation. Immunity 38:694–704 [Google Scholar]
141. Possot C, Schmutz S, Chea S, Boucontet L, Louise A. 141.  et al. 2011. Notch signaling is necessary for adult, but not fetal, development of RORγt⁺ innate lymphoid cells. Nat. Immunol. 12:949–58 [Google Scholar]
142. Lee JS, Cella M, McDonald KG, Garlanda C, Kennedy GD. 142.  et al. 2012. AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on and independent of Notch. Nat. Immunol. 13:144–51 [Google Scholar]
143. Garbe AI, Krueger A, Gounari F, Zuniga-Pflucker JC, von Boehmer H. 143.  2006. Differential synergy of Notch and T cell receptor signaling determines αβ versus γΔ lineage fate. J. Exp. Med. 203:1579–90 [Google Scholar]
144. Ikawa T, Fujimoto S, Kawamoto H, Katsura Y, Yokota Y. 144.  2001. Commitment to natural killer cells requires the helix-loop-helix inhibitor Id2. PNAS 98:5164–69 [Google Scholar]
145. Carotta S, Pang SH, Nutt SL, Belz GT. 145.  2011. Identification of the earliest NK-cell precursor in the mouse BM. Blood 117:5449–52 [Google Scholar]
146. Kim JK, Takeuchi M, Yokota Y. 146.  2004. Impairment of intestinal intraepithelial lymphocytes in Id2 deficient mice. Gut 53:480–86 [Google Scholar]
147. Yamagata T, Benoist C, Mathis D. 147.  2006. A shared gene-expression signature in innate-like lymphocytes. Immunol. Rev. 210:52–66 [Google Scholar]
148. Monticelli LA, Yang Y, Knell J, D'Cruz LM, Cannarile MA. 148.  et al. 2009. Transcriptional regulator Id2 controls survival of hepatic NKT cells. PNAS 106:19461–66 [Google Scholar]
149. Zhang B, Lin YY, Dai M, Zhuang Y. 149.  2014. Id3 and Id2 act as a dual safety mechanism in regulating the development and population size of innate-like γΔ T cells. J. Immunol. 192:1055–63 [Google Scholar]
150. Vosshenrich CA, Garcia-Ojeda ME, Samson-Villeger SI, Pasqualetto V, Enault L. 150.  et al. 2006. A thymic pathway of mouse natural killer cell development characterized by expression of GATA-3 and CD127. Nat. Immunol. 7:1217–24 [Google Scholar]
151. Gascoyne DM, Long E, Veiga-Fernandes H, de Boer J, Williams O. 151.  et al. 2009. The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development. Nat. Immunol. 10:1118–24 [Google Scholar]
152. Seillet C, Huntington ND, Gangatirkar P, Axelsson E, Minnich M. 152.  et al. 2014. Differential requirement for Nfil3 during NK cell development. J. Immunol. 192:2667–76 [Google Scholar]
153. Male V, Nisoli I, Kostrzewski T, Allan DS, Carlyle JR. 153.  et al. 2014. The transcription factor E4bp4/Nfil3 controls commitment to the NK lineage and directly regulates Eomes and Id2 expression. J. Exp. Med. 211:635–42 [Google Scholar]
154. Yu X, Rollins D, Ruhn KA, Stubblefield JJ, Green CB. 154.  et al. 2013. TH17 cell differentiation is regulated by the circadian clock. Science 342:727–30 [Google Scholar]
155. Seillet C, Rankin LC, Groom JR, Mielke LA, Tellier J. 155.  et al. 2014. Nfil3 is required for the development of all innate lymphoid cell subsets. J. Exp. Med. 211:1733–40 [Google Scholar]
156. Geiger TL, Abt MC, Gasteiger G, Firth MA, O'Connor MH. 156.  et al. 2014. Nfil3 is crucial for development of innate lymphoid cells and host protection against intestinal pathogens. J. Exp. Med. 211:1723–31 [Google Scholar]
157. Aliahmad P, de la Torre B, Kaye J. 157.  2010. Shared dependence on the DNA-binding factor TOX for the development of lymphoid tissue-inducer cell and NK cell lineages. Nat. Immunol. 11:945–52 [Google Scholar]
158. Aliahmad P, Kadavallore A, de la Torre B, Kappes D, Kaye J. 158.  2011. TOX is required for development of the CD4 T cell lineage gene program. J. Immunol. 187:5931–40 [Google Scholar]
159. Kang J, Coles M. 159.  2012. IL-7: the global builder of the innate lymphoid network and beyond, one niche at a time. Semin. Immunol. 24:190–97 [Google Scholar]
160. Narayan K, Kang J. 160.  2010. Disorderly conduct in γΔ versus αβ T cell lineage commitment. Semin. Immunol. 22:222–27 [Google Scholar]
161. Shibata K, Yamada H, Nakamura M, Hatano S, Katsuragi Y. 161.  et al. 2014. IFN-γ-producing and IL-17-producing γΔ T cells differentiate at distinct developmental stages in murine fetal thymus. J. Immunol. 192:2210–18 [Google Scholar]
162. Bowles J, Schepers G, Koopman P. 162.  2000. Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev. Biol. 227:239–55 [Google Scholar]
163. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR. 163.  et al. 2009. Diversity and complexity in DNA recognition by transcription factors. Science 324:1720–23 [Google Scholar]
164. Melichar HJ, Narayan K, Der SD, Hiraoka Y, Gardiol N. 164.  et al. 2007. Regulation of γΔ versus αβ T lymphocyte differentiation by the transcription factor SOX13. Science 315:230–33 [Google Scholar]
165. Turchinovich G, Hayday AC. 165.  2011. Skint-1 identifies a common molecular mechanism for the development of interferon-γ-secreting versus interleukin-17-secreting γΔ T cells. Immunity 35:59–68 [Google Scholar]
166. Wang R, Xie H, Huang Z, Ma J, Fang X. 166.  et al. 2011. T cell factor 1 regulates thymocyte survival via a RORγt-dependent pathway. J. Immunol. 187:5964–73 [Google Scholar]
167. Keerthivasan S, Aghajani K, Dose M, Molinero L, Khan MW. 167.  et al. 2014. β-Catenin promotes colitis and colon cancer through imprinting of proinflammatory properties in T cells. Sci. Transl. Med. 6:225ra28 [Google Scholar]
168. Tanaka S, Suto A, Iwamoto T, Kashiwakuma D, Kagami S. 168.  et al. 2014. Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3. J. Exp. Med. 211:1857–74 [Google Scholar]
169. Shim S, Kwan KY, Li M, Lefebvre V, Sestan N. 169.  2012. Cis-regulatory control of corticospinal system development and evolution. Nature 486:74–79 [Google Scholar]
170. Schilham MW, Oosterwegel MA, Moerer P, Ya J, de Boer PA. 170.  et al. 1996. Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380:711–14 [Google Scholar]
171. Spooner CJ, Lesch J, Yan D, Khan AA, Abbas A. 171.  et al. 2013. Specification of type 2 innate lymphocytes by the transcriptional determinant Gfi1. Nat. Immunol. 14:1229–36 [Google Scholar]
172. Cohen NR, Brennan PJ, Shay T, Watts GF, Brigl M. 172.  et al. 2013. Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nat. Immunol. 14:90–99 [Google Scholar]
173. Sinner D, Kordich JJ, Spence JR, Opoka R, Rankin S. 173.  et al. 2007. Sox17 and Sox4 differentially regulate beta-catenin/T-cell factor activity and proliferation of colon carcinoma cells. Mol. Cell. Biol. 27:7802–15 [Google Scholar]
174. Yu Q, Sharma A, Ghosh A, Sen JM. 174.  2011. T cell factor-1 negatively regulates expression of IL-17 family of cytokines and protects mice from experimental autoimmune encephalomyelitis. J. Immunol. 186:3946–52 [Google Scholar]
175. Wei G, Abraham BJ, Yagi R, Jothi R, Cui K. 175.  et al. 2011. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35:299–311 [Google Scholar]
176. Vahedi G, Takahashi H, Nakayamada S, Sun HW, Sartorelli V. 176.  et al. 2012. STATs shape the active enhancer landscape of T cell populations. Cell 151:981–93 [Google Scholar]
177. Zhu J, Jankovic D, Oler AJ, Wei G, Sharma S. 177.  et al. 2012. The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses. Immunity 37:660–73 [Google Scholar]
178. Murphy TL, Tussiwand R, Murphy KM. 178.  2013. Specificity through cooperation: BATF-IRF interactions control immune-regulatory networks. Nat. Rev. Immunol. 13:499–509 [Google Scholar]
179. Esser C, Rannug A, Stockinger B. 179.  2009. The aryl hydrocarbon receptor in immunity. Trends Immunol. 30:447–54 [Google Scholar]
180. Muranski P, Borman ZA, Kerkar SP, Klebanoff CA, Ji Y. 180.  et al. 2011. Th17 cells are long lived and retain a stem cell-like molecular signature. Immunity 35:972–85 [Google Scholar]
181. Bailis W, Yashiro-Ohtani Y, Fang TC, Hatton RD, Weaver CT. 181.  et al. 2013. Notch simultaneously orchestrates multiple helper T cell programs independently of cytokine signals. Immunity 39:148–59 [Google Scholar]
182. Yu Q, Sharma A, Oh SY, Moon HG, Hossain MZ. 182.  et al. 2009. T cell factor 1 initiates the T helper type 2 fate by inducing the transcription factor GATA-3 and repressing interferon-gamma. Nat. Immunol. 10:992–99 [Google Scholar]
183. Kuwahara M, Yamashita M, Shinoda K, Tofukuji S, Onodera A. 183.  et al. 2012. The transcription factor Sox4 is a downstream target of signaling by the cytokine TGF-beta and suppresses T_H2 differentiation. Nat. Immunol. 13:778–86 [Google Scholar]
184. Jeannet G, Boudousquie C, Gardiol N, Kang J, Huelsken J, Held W. 184.  2010. Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. PNAS 107:9777–82 [Google Scholar]
185. Zhou X, Yu S, Zhao DM, Harty JT, Badovinac VP, Xue HH. 185.  2010. Differentiation and persistence of memory CD8⁺ T cells depend on T cell factor 1. Immunity 33:229–40 [Google Scholar]
186. Miyazaki M, Rivera RR, Miyazaki K, Lin YC, Agata Y, Murre C. 186.  2011. 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 [Google Scholar]
187. Yang CY, Best JA, Knell J, Yang E, Sheridan AD. 187.  et al. 2011. The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8⁺ T cell subsets. Nat. Immunol. 12:1221–29 [Google Scholar]
188. Yu Q, Erman B, Park JH, Feigenbaum L, Singer A. 188.  2004. IL-7 receptor signals inhibit expression of transcription factors TCF-1, LEF-1, and RORγt: impact on thymocyte development. J. Exp. Med. 200:797–803 [Google Scholar]
189. Rawlings JS, Gatzka M, Thomas PG, Ihle JN. 189.  2011. Chromatin condensation via the condensin II complex is required for peripheral T-cell quiescence. EMBO J. 30:263–76 [Google Scholar]
190. Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM, Degnan BM. 190.  2008. Genesis and expansion of metazoan transcription factor gene classes. Mol. Biol. Evol. 25:980–96 [Google Scholar]
191. Nichols SA, Dirks W, Pearse JS, King N. 191.  2006. Early evolution of animal cell signaling and adhesion genes. PNAS 103:12451–56 [Google Scholar]
192. Kortschak RD, Samuel G, Saint R, Miller DJ. 192.  2003. EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr. Biol. 13:2190–95 [Google Scholar]
193. Hirano M, Guo P, McCurley N, Schorpp M, Das S. 193.  et al. 2013. Evolutionary implications of a third lymphocyte lineage in lampreys. Nature 501:435–38 [Google Scholar]
194. Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG. 194.  et al. 2007. Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat. Immunol. 8:647–56 [Google Scholar]
195. Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N. 195.  et al. 2013. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat. Genet. 45:415–21 [Google Scholar]
196. Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP. 196.  2006. An ancient evolutionary origin of the Rag1/2 gene locus. PNAS 103:3728–33 [Google Scholar]
197. Sebe-Pedros A, de Mendoza A, Lang BF, Degnan BM, Ruiz-Trillo I. 197.  2011. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol. Biol. Evol. 28:1241–54 [Google Scholar]
198. Ryan JF, Baxevanis AD. 198.  2007. Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla. Biol. Direct 2:37 [Google Scholar]
199. Suga H, Chen Z, de Mendoza A, Sebe-Pedros A, Brown MW. 199.  et al. 2013. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4:2325 [Google Scholar]
200. King N, Westbrook MJ, Young SL, Kuo A, Abedin M. 200.  et al. 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783–88 [Google Scholar]
201. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME. 201.  et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:720–26 [Google Scholar]
202. Leininger S, Adamski M, Bergum B, Guder C, Liu J. 202.  et al. 2014. Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat. Commun. 5:3905 [Google Scholar]
203. Jager M, Queinnec E, Houliston E, Manuel M. 203.  2006. Expansion of the SOX gene family predated the emergence of the Bilateria. Mol. Phylogenet. Evol. 39:468–77 [Google Scholar]
204. Fortunato S, Adamski M, Bergum B, Guder C, Jordal S. 204.  et al. 2012. Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns. EvoDevo 3:14 [Google Scholar]
205. Hoy MA, Yu F, Meyer JM, Tarazona OA, Jeyaprakash A, Wu K. 205.  2013. Transcriptome sequencing and annotation of the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae): a cautionary tale about possible contamination by prey sequences. Exp. Appl. Acarol. 59:283–96 [Google Scholar]
206. Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P. 206.  et al. 2007. Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. BMC Evol. Biol. 7:33 [Google Scholar]
207. Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH. 207.  et al. 2006. The immune gene repertoire encoded in the purple sea urchin genome. Dev. Biol. 300:349–65 [Google Scholar]
208. Rast JP, Smith LC, Loza-Coll M, Hibino T, Litman GW. 208.  2006. Genomic insights into the immune system of the sea urchin. Science 314:952–56 [Google Scholar]
209. Solek CM, Oliveri P, Loza-Coll M, Schrankel CS, Ho EC. 209.  et al. 2013. An ancient role for Gata-1/2/3 and Scl transcription factor homologs in the development of immunocytes. Dev. Biol. 382:280–92 [Google Scholar]
210. Yamada L, Kobayashi K, Degnan B, Satoh N, Satou Y. 210.  2003. A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev. Genes Evol. 213:245–53 [Google Scholar]
211. Sebe-Pedros A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A. 211.  et al. 2013. Early evolution of the T-box transcription factor family. PNAS 110:16050–55 [Google Scholar]
212. Horton AC, Gibson-Brown JJ. 212.  2002. Evolution of developmental functions by the Eomesodermin, T-brain-1, Tbx21 subfamily of T-box genes: insights from amphioxus. J. Exp. Zool. 294:112–21 [Google Scholar]
213. Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM. 213.  et al. 2014. Elephant shark genome provides unique insights into gnathostome evolution. Nature 505:174–79 [Google Scholar]
214. Zhang T, Xiong H, Kan LX, Zhang CK, Jiao XF. 214.  et al. 1999. Genomic sequence, structural organization, molecular evolution, and aberrant rearrangement of promyelocytic leukemia zinc finger gene. PNAS 96:11422–27 [Google Scholar]
215. Howard RM, Sundaram MV. 215.  2002. C. elegans EOR-1/PLZF and EOR-2 positively regulate Ras and Wnt signaling and function redundantly with LIN-25 and the SUR-2 Mediator component. Genes Dev. 16:1815–27 [Google Scholar]
216. Maeng O, Son W, Chung J, Lee KS, Lee YH. 216.  et al. 2012. The BTB/POZ-ZF transcription factor dPLZF is involved in Ras/ERK signaling during Drosophila wing development. Mol. Cells 33:457–63 [Google Scholar]
217. Imai KS, Hino K, Yagi K, Satoh N, Satou Y. 217.  2004. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development 131:4047–58 [Google Scholar]
218. Kosan C, Saba I, Godmann M, Herold S, Herkert B. 218.  et al. 2010. Transcription factor miz-1 is required to regulate interleukin-7 receptor signaling at early commitment stages of B cell differentiation. Immunity 33:917–28 [Google Scholar]
219. Jetten AM. 219.  2009. Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism. Nucl. Recept. Signal. 7:e003 [Google Scholar]
220. Wang Y, Kumar N, Solt LA, Richardson TI, Helvering LM. 220.  et al. 2010. Modulation of retinoic acid receptor-related orphan receptor alpha and gamma activity by 7-oxygenated sterol ligands. J. Biol. Chem. 285:5013–25 [Google Scholar]
221. Monte MM, Wang T, Costa MM, Harun NO, Secombes CJ. 221.  2012. Cloning and expression analysis of two ROR-γ homologues (ROR-γa1 and ROR-γa2) in rainbow trout Oncorhynchus mykiss. Fish Shellfish Immunol. 33:365–74 [Google Scholar]
222. Egawa T, Eberl G, Taniuchi I, Benlagha K, Geissmann F. 222.  et al. 2005. Genetic evidence supporting selection of the Vα14i NKT cell lineage from double-positive thymocyte precursors. Immunity 22:705–16 [Google Scholar]
223. Du L, Yang X, Yang L, Wang X, Zhang A, Zhou H. 223.  2012. Molecular evidence for the involvement of RORα and RORγ in immune response in teleost. Fish Shellfish Immunol. 33:418–26 [Google Scholar]
224. Hymowitz SG, Filvaroff EH, Yin JP, Lee J, Cai L. 224.  et al. 2001. IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding. EMBO J. 20:5332–41 [Google Scholar]
225. Roberts S, Gueguen Y, de Lorgeril J, Goetz F. 225.  2008. Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure. Dev. Comp. Immunol. 32:1099–104 [Google Scholar]
226. Li J, Zhang Y, Zhang Y, Xiang Z, Tong Y. 226.  et al. 2014. Genomic characterization and expression analysis of five novel IL-17 genes in the Pacific oyster, Crassostrea gigas. Fish Shellfish Immunol. 40:455–65 [Google Scholar]
227. Ramirez-Carrozzi V, Sambandam A, Luis E, Lin Z, Jeet S. 227.  et al. 2011. IL-17C regulates the innate immune function of epithelial cells in an autocrine manner. Nat. Immunol. 12:1159–66 [Google Scholar]
228. Tsutsui S, Nakamura O, Watanabe T. 228.  2007. Lamprey (Lethenteron japonicum) IL-17 upregulated by LPS-stimulation in the skin cells. Immunogenetics 59:873–82 [Google Scholar]
229. Bar E, Whitney PG, Moor K, Reis e Sousa C, LeibundGut-Landmann S. 229.  2014. IL-17 regulates systemic fungal immunity by controlling the functional competence of NK cells. Immunity 40:117–27 [Google Scholar]
230. Goetz FW, Planas JV, MacKenzie S. 230.  2004. Tumor necrosis factors. Dev. Comp. Immunol. 28:487–97 [Google Scholar]
231. Rangel-Moreno J, Carragher DM, de la Luz Garcia-Hernandez M, Hwang JY, Kusser K. 231.  et al. 2011. The development of inducible bronchus-associated lymphoid tissue depends on IL-17. Nat. Immunol. 12:639–46 [Google Scholar]
232. Miller DJ, Hemmrich G, Ball EE, Hayward DC, Khalturin K. 232.  et al. 2007. The innate immune repertoire in Cnidaria—ancestral complexity and stochastic gene loss. Genome Biol. 8:R59 [Google Scholar]
233. Ikuta K, Kina T, MacNeil I, Uchida N, Peault B. 233.  et al. 1990. A developmental switch in thymic lymphocyte maturation potential occurs at the level of hematopoietic stem cells. Cell 62:863–74 [Google Scholar]
234. Ramond C, Berthault C, Burlen-Defranoux O, de Sousa AP, Guy-Grand D. 234.  et al. 2014. Two waves of distinct hematopoietic progenitor cells colonize the fetal thymus. Nat. Immunol. 15:27–35 [Google Scholar]
235. Rose S, Lichtenheld M, Foote MR, Adkins B. 235.  2007. Murine neonatal CD4⁺ cells are poised for rapid Th2 effector-like function. J. Immunol. 178:2667–78 [Google Scholar]
236. Sieweke MH, Allen JE. 236.  2013. Beyond stem cells: self-renewal of differentiated macrophages. Science 342:1242974 [Google Scholar]
237. Medvinsky A, Rybtsov S, Taoudi S. 237.  2011. Embryonic origin of the adult hematopoietic system: advances and questions. Development 138:1017–31 [Google Scholar]
238. Kumaravelu P, Hook L, Morrison AM, Ure J, Zhao S. 238.  et al. 2002. Quantitative developmental anatomy of definitive haematopoietic stem cells/long-term repopulating units (HSC/RUs): role of the aorta-gonad-mesonephros (AGM) region and the yolk sac in colonisation of the mouse embryonic liver. Development 129:4891–99 [Google Scholar]
239. Yoshimoto M, Porayette P, Glosson NL, Conway SJ, Carlesso N. 239.  et al. 2012. Autonomous murine T-cell progenitor production in the extra-embryonic yolk sac before HSC emergence. Blood 119:5706–14 [Google Scholar]
240. Boiers C, Carrelha J, Lutteropp M, Luc S, Green JC. 240.  et al. 2013. Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell Stem Cell 13:535–48 [Google Scholar]
241. Tang Y, Peitzsch C, Charoudeh HN, Cheng M, Chaves P. 241.  et al. 2012. Emergence of NK-cell progenitors and functionally competent NK-cell lineage subsets in the early mouse embryo. Blood 120:63–75 [Google Scholar]
242. Sojka DK, Plougastel-Douglas B, Yang L, Pak-Wittel MA, Artyomov MN. 242.  et al. 2014. Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells. eLife 3:e01659 [Google Scholar]
243. Michie AM, Carlyle JR, Schmitt TM, Ljutic B, Cho SK. 243.  et al. 2000. Clonal characterization of a bipotent T cell and NK cell progenitor in the mouse fetal thymus. J. Immunol. 164:1730–33 [Google Scholar]
244. Douagi I, Colucci F, Di Santo JP, Cumano A. 244.  2002. Identification of the earliest prethymic bipotent T/NK progenitor in murine fetal liver. Blood 99:463–71 [Google Scholar]
245. Gilfillan S, Benoist C, Mathis D. 245.  1995. Mice lacking terminal deoxynucleotidyl transferase: adult mice with a fetal antigen receptor repertoire. Immunol. Rev. 148:201–19 [Google Scholar]
246. Herzenberg LA, Herzenberg LA. 246.  1989. Toward a layered immune system. Cell 59:953–54 [Google Scholar]
247. Xiong N, Kang C, Raulet DH. 247.  2002. Redundant and unique roles of two enhancer elements in the TCRγ locus in gene regulation and γΔ T cell development. Immunity 16:453–63 [Google Scholar]
248. Roberts NA, White AJ, Jenkinson WE, Turchinovich G, Nakamura K. 248.  et al. 2012. Rank signaling links the development of invariant γΔ T cell progenitors and Aire⁺ medullary epithelium. Immunity 36:427–37 [Google Scholar]
249. Haas JD, Ravens S, Duber S, Sandrock I, Oberdorfer L. 249.  et al. 2012. Development of interleukin-17-producing γΔ T cells is restricted to a functional embryonic wave. Immunity 37:48–59 [Google Scholar]
250. Kim I, Saunders TL, Morrison SJ. 250.  2007. Sox17 dependence distinguishes the transcriptional regulation of fetal from adult hematopoietic stem cells. Cell 130:470–83 [Google Scholar]
251. Wang JH, Nichogiannopoulou A, Wu L, Sun L, Sharpe AH. 251.  et al. 1996. Selective defects in the development of the fetal and adult lymphoid system in mice with an Ikaros null mutation. Immunity 5:537–49 [Google Scholar]
252. Yuan J, Nguyen CK, Liu X, Kanellopoulou C, Muljo SA. 252.  2012. Lin28b reprograms adult bone marrow hematopoietic progenitors to mediate fetal-like lymphopoiesis. Science 335:1195–200 [Google Scholar]
253. McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT. 253.  et al. 2012. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell 11:701–14 [Google Scholar]
254. Shyh-Chang N, Daley GQ. 254.  2013. Lin28: primal regulator of growth and metabolism in stem cells. Cell Stem Cell 12:395–406 [Google Scholar]
255. Copley MR, Babovic S, Benz C, Knapp DJ, Beer PA. 255.  et al. 2013. The Lin28b-let-7-Hmga2 axis determines the higher self-renewal potential of fetal haematopoietic stem cells. Nat. Cell Biol. 15:916–25 [Google Scholar]
256. Martins VC, Ruggiero E, Schlenner SM, Madan V, Schmidt M. 256.  et al. 2012. Thymus-autonomous T cell development in the absence of progenitor import. J. Exp. Med. 209:1409–17 [Google Scholar]
257. Peaudecerf L, Lemos S, Galgano A, Krenn G, Vasseur F. 257.  et al. 2012. Thymocytes may persist and differentiate without any input from bone marrow progenitors. J. Exp. Med. 209:1401–8 [Google Scholar]
258. He S, Kim I, Lim MS, Morrison SJ. 258.  2011. Sox17 expression confers self-renewal potential and fetal stem cell characteristics upon adult hematopoietic progenitors. Genes Dev. 25:1613–27 [Google Scholar]