Lung Endoderm Morphogenesis: Gasping for Form and Function

Literature Cited

1. Ang SL, Rossant J. 1994. HNF-3β is essential for node and notochord formation in mouse development. Cell 78:561–74 [Google Scholar]
2. Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M. et al. 2013. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 12:699–712 [Google Scholar]
3. Banerjee A, Trivedi CM, Damera G, Jiang M, Jester W. et al. 2012. Trichostatin A abrogates airway constriction, but not inflammation, in murine and human asthma models. Am. J. Respir. Cell Mol. Biol. 46:132–38 [Google Scholar]
4. Barkauskas CE, Cronce MJ, Rackley CR, Bowie EJ, Keene DR. et al. 2013. Type 2 alveolar cells are stem cells in adult lung. J. Clin. Investig. 123:3025–36 [Google Scholar]
5. Batista PJ, Chang HY. 2013. Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–307 [Google Scholar]
6. Bauer CR, Hartl TA, Bosco G. 2012. Condensin II promotes the formation of chromosome territories by inducing axial compaction of polyploid interphase chromosomes. PLOS Genet. 8:e1002873 [Google Scholar]
7. Bellusci S, Furuta Y, Rush MG, Henderson R, Winnier G, Hogan BL. 1997. Involvement of Sonic hedgehog (Shh) in mouse embryonic lung growth and morphogenesis. Development 124:53–63 [Google Scholar]
8. Benlhabib H, Mendelson CR. 2011. Epigenetic regulation of surfactant protein A gene (SP-A) expression in fetal lung reveals a critical role for Suv39h methyltransferases during development and hypoxia. Mol. Cell. Biol. 31:1949–58 [Google Scholar]
9. Bickmore WA. 2013. The spatial organization of the human genome. Annu. Rev. Genomics Hum. Genet. 14:67–84 [Google Scholar]
10. Bostrom H, Willetts K, Pekny M, Leveen P, Lindahl P. et al. 1996. PDGF-A signaling is a critical event in lung alveolar myofibroblast development and alveogenesis. Cell 85:863–73 [Google Scholar]
11. Cardoso WV, Lü J. 2006. Regulation of early lung morphogenesis: questions, facts and controversies. Development 133:1611–24 [Google Scholar]
12. Carraro G, El-Hashash A, Guidolin D, Tiozzo C, Turcatel G. et al. 2009. miR-17 family of microRNAs controls FGF10-mediated embryonic lung epithelial branching morphogenesis through MAPK14 and STAT3 regulation of E-Cadherin distribution. Dev. Biol. 333:238–50 [Google Scholar]
13. Cech TR, Steitz JA. 2014. The noncoding RNA revolution—trashing old rules to forge new ones. Cell 157:77–94 [Google Scholar]
14. Chang DR, Martinez Alanis D, Miller RK, Ji H, Akiyama H. et al. 2013. Lung epithelial branching program antagonizes alveolar differentiation. PNAS 110:18042–51 [Google Scholar]
15. Chapman DL, Garvey N, Hancock S, Alexiou M, Agulnik SI. et al. 1996. Expression of the T-box family genes, Tbx1–Tbx5, during early mouse development. Dev. Dyn. 206:379–90 [Google Scholar]
16. Chen J, Knowles HJ, Hebert JL, Hackett BP. 1998. Mutation of the mouse hepatocyte nuclear factor/forkhead homologue 4 gene results in an absence of cilia and random left-right asymmetry. J. Clin. Investig. 102:1077–82 [Google Scholar]
17. Chen J, Krasnow MA. 2012. Integrin β1 suppresses multilayering of a simple epithelium. PLOS ONE 7e52886
18. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M. et al. 2009. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:834–40 [Google Scholar]
19. Chuang PT, Kawcak T, McMahon AP. 2003. Feedback control of mammalian Hedgehog signaling by the Hedgehog-binding protein, Hip1, modulates Fgf signaling during branching morphogenesis of the lung. Genes Dev. 17:342–47 [Google Scholar]
20. Colebatch HJ, Ng CK. 1992. Estimating alveolar surface area during life. Respir. Physiol. 88:163–70 [Google Scholar]
21. Dakhlallah D, Batte K, Wang Y, Cantemir-Stone CZ, Yan P. et al. 2013. Epigenetic regulation of miR-17∼92 contributes to the pathogenesis of pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 187:397–405 [Google Scholar]
22. Daniels CB, Orgeig S, Sullivan LC, Ling N, Bennett MB. et al. 2004. The origin and evolution of the surfactant system in fish: insights into the evolution of lungs and swim bladders. Physiol. Biochem. Zool. 77:732–49 [Google Scholar]
23. De Langhe SP, Sala FG, Del Moral PM, Fairbanks TJ, Yamada KM. et al. 2005. Dickkopf-1 (DKK1) reveals that fibronectin is a major target of Wnt signaling in branching morphogenesis of the mouse embryonic lung. Dev. Biol. 277:316–31 [Google Scholar]
24. de Wit E, Bouwman BA, Zhu Y, Klous P, Splinter E. et al. 2013. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501:227–31 [Google Scholar]
25. Denholtz M, Plath K. 2012. Pluripotency in 3D: genome organization in pluripotent cells. Curr. Opin. Cell Biol. 24:793–801 [Google Scholar]
26. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S. et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22:1775–89 [Google Scholar]
27. Desai TJ, Chen F, Lu J, Qian J, Niederreither K. et al. 2006. Distinct roles for retinoic acid receptors α and β in early lung morphogenesis. Dev. Biol. 291:12–24 [Google Scholar]
28. Desai TJ, Malpel S, Flentke GR, Smith SM, Cardoso WV. 2004. Retinoic acid selectively regulates Fgf10 expression and maintains cell identity in the prospective lung field of the developing foregut. Dev. Biol. 273:402–15 [Google Scholar]
29. Domyan ET, Ferretti E, Throckmorton K, Mishina Y, Nicolis SK, Sun X. 2011. Signaling through BMP receptors promotes respiratory identity in the foregut via repression of Sox2. Development 138:971–81 [Google Scholar]
30. Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ. et al. 2008. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2:437–47 [Google Scholar]
31. Eissmann M, Gutschner T, Hammerle M, Gunther S, Caudron-Herger M. et al. 2012. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 9:1076–87 [Google Scholar]
32. ENCODE Proj. Consort 2004. The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306:636–40 [Google Scholar]
33. Gomez-Diaz E, Corces VG. 2014. Architectural proteins: regulators of 3D genome organization in cell fate. Trends Cell Biol. 24:703–11 [Google Scholar]
34. Goss AM, Tian Y, Tsukiyama T, Cohen ED, Zhou D. et al. 2009. Wnt2/2b and β-catenin signaling are necessary and sufficient to specify lung progenitors in the foregut. Dev. Cell 17:290–8 [Google Scholar]
35. Green MD, Chen A, Nostro MC, d'Souza SL, Schaniel C. et al. 2011. Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells. Nat. Biotechnol. 29:267–72 [Google Scholar]
36. Grote P, Herrmann BG. 2013. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 10:1579–85 [Google Scholar]
37. Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S. et al. 2013. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev. Cell 24:206–14 [Google Scholar]
38. Guseh JS, Bores SA, Stanger BZ, Zhou Q, Anderson WJ. et al. 2009. Notch signaling promotes airway mucous metaplasia and inhibits alveolar development. Development 136:1751–59 [Google Scholar]
39. Gutschner T, Hammerle M, Diederichs S. 2013. MALAT1—a paradigm for long noncoding RNA function in cancer. J. Mol. Med. 91:791–801 [Google Scholar]
40. Harris KS, Zhang Z, McManus MT, Harfe BD, Sun X. 2006. Dicer function is essential for lung epithelium morphogenesis. PNAS 103:2208–13 [Google Scholar]
41. Harris-Johnson KS, Domyan ET, Vezina CM, Sun X. 2009. β-Catenin promotes respiratory progenitor identity in mouse foregut. PNAS 106:16287–92 [Google Scholar]
42. Heine UI, Munoz EF, Flanders KC, Roberts AB, Sporn MB. 1990. Colocalization of TGF-β1 and collagen I and III, fibronectin and glycosaminoglycans during lung branching morphogenesis. Development 109:29–36 [Google Scholar]
43. Herriges MJ, Morrisey EE. 2014. Lung development: orchestrating the generation and regeneration of a complex organ. Development 141:502–13 [Google Scholar]
44. Herriges MJ, Swarr DT, Morley MP, Rathi KS, Peng T. et al. 2014. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev. 28:1363–79 [Google Scholar]
45. Hill DA, Ivanovich J, Priest JR, Gurnett CA, Dehner LP. et al. 2009. DICER1 mutations in familial pleuropulmonary blastoma. Science 325:965 [Google Scholar]
46. Hogan BLM, Barkauskas CE, Chapman HA, Epstein JA, Jain R. et al. 2014. Repair and regeneration of the respiratory system: complexity, plasticity, and mechanisms of lung stem cell function. Stem Cell 15:123–38 [Google Scholar]
47. Huang SX, Green MD, de Carvalho AT, Mumau M, Chen YW. et al. 2015. The in vitro generation of lung and airway progenitor cells from human pluripotent stem cells. Nat. Protoc. 10:413–25 [Google Scholar]
48. Huang SX, Islam MN, O'Neill J, Hu Z, Yang YG. et al. 2014. Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nat. Biotechnol. 32:84–91 [Google Scholar]
49. Hui CC, Slusarski D, Platt KA, Holmgren R, Joyner AL. 1994. Expression of three mouse homologs of the Drosophila segment polarity gene cubitus interruptus, Gli, Gli-2, and Gli-3, in ectoderm- and mesoderm-derived tissues suggests multiple roles during postimplantation development. Dev. Biol. 162:402–13 [Google Scholar]
50. Ito K, Caramori G, Lim S, Oates T, Chung KF. et al. 2002. Expression and activity of histone deacetylases in human asthmatic airways. Am. J. Respir. Crit. Care Med. 166:392–96 [Google Scholar]
51. Ito K, Yamamura S, Essilfie-Quaye S, Cosio B, Ito M. et al. 2006. Histone deacetylase 2–mediated deacetylation of the glucocorticoid receptor enables NF-κB suppression. J. Exp. Med. 203:7–13 [Google Scholar]
52. Kadzik RS, Cohen ED, Morley MP, Stewart KM, Lu MM, Morrisey EE. 2014. Wnt ligand/Frizzled 2 receptor signaling regulates tube shape and branch-point formation in the lung through control of epithelial cell shape. PNAS 111:12444–49 [Google Scholar]
53. Kageyama R, Ohtsuka T, Shimojo H, Imayoshi I. 2008. Dynamic Notch signaling in neural progenitor cells and a revised view of lateral inhibition. Nat. Neurosci. 11:1247–51 [Google Scholar]
54. Kalb JM, Lau KK, Goszczynski B, Fukushige T, Moons D. et al. 1998. pha-4 is Ce-fkh-1, a fork head/HNF-3α,β,γ homolog that functions in organogenesis of the C. elegans pharynx. Development 125:2171–80 [Google Scholar]
55. Kalinichenko VV, Lim L, Stolz DB, Shin B, Rausa FM. et al. 2001. Defects in pulmonary vasculature and perinatal lung hemorrhage in mice heterozygous null for the Forkhead Box f1 transcription factor. Dev. Biol. 235:489–506 [Google Scholar]
56. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A. et al. 2014. Defining functional DNA elements in the human genome. PNAS 111:6131–38 [Google Scholar]
57. Kim HY, Varner VD, Nelson CM. 2013. Apical constriction initiates new bud formation during monopodial branching of the embryonic chicken lung. Development 140:3146–55 [Google Scholar]
58. Kotton DN, Morrisey EE. 2014. Lung regeneration: mechanisms, applications and emerging stem cell populations. Nat. Med. 20:822–32 [Google Scholar]
59. Lebeche D, Malpel S, Cardoso WV. 1999. Fibroblast growth factor interactions in the developing lung. Mech. Dev. 86:125–36 [Google Scholar]
60. Lee JH, Bhang DH, Beede A, Huang TL, Stripp BR. et al. 2014. Lung stem cell differentiation in mice directed by endothelial cells via a BMP4-NFATc1-thrombospondin-1 axis. Cell 156:440–55 [Google Scholar]
61. Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D. et al. 2014. Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature 508:345–50 [Google Scholar]
62. Letterio JJ, Geiser AG, Kulkarni AB, Roche NS, Sporn MB, Roberts AB. 1994. Maternal rescue of transforming growth factor-β1 null mice. Science 264:1936–38 [Google Scholar]
63. Li Y, Zhang H, Choi SC, Litingtung Y, Chiang C. 2004. Sonic hedgehog signaling regulates Gli3 processing, mesenchymal proliferation, and differentiation during mouse lung organogenesis. Dev. Biol. 270:214–31 [Google Scholar]
64. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T. et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–93 [Google Scholar]
65. Lindahl P, Karlsson L, Hellstrom M, Gebre-Medhin S, Willetts K. et al. 1997. Alveogenesis failure in PDGF-A-deficient mice is coupled to lack of distal spreading of alveolar smooth muscle cell progenitors during lung development. Development 124:3943–53 [Google Scholar]
66. Lize M, Herr C, Klimke A, Bals R, Dobbelstein M. 2010a. MicroRNA-449a levels increase by several orders of magnitude during mucociliary differentiation of airway epithelia. Cell Cycle 9:4579–83 [Google Scholar]
67. Lize M, Pilarski S, Dobbelstein M. 2010b. E2F1-inducible microRNA 449a/b suppresses cell proliferation and promotes apoptosis. Cell Death Differ. 17:452–58 [Google Scholar]
68. Londhe VA, Sundar IK, Lopez B, Maisonet TM, Yu Y. et al. 2011. Hyperoxia impairs alveolar formation and induces senescence through decreased histone deacetylase activity and up-regulation of p21 in neonatal mouse lung. Pediatr. Res. 69:371–77 [Google Scholar]
69. Longmire TA, Ikonomou L, Hawkins F, Christodoulou C, Cao Y. et al. 2012. Efficient derivation of purified lung and thyroid progenitors from embryonic stem cells. Cell Stem Cell 10:398–411 [Google Scholar]
70. Lu J, Izvolsky KI, Qian J, Cardoso WV. 2005. Identification of FGF10 targets in the embryonic lung epithelium during bud morphogenesis. J. Biol. Chem. 280:4834–41 [Google Scholar]
71. Lu Y, Thomson JM, Wong HY, Hammond SM, Hogan BL. 2007. Transgenic over-expression of the microRNA miR-17-92 cluster promotes proliferation and inhibits differentiation of lung epithelial progenitor cells. Dev. Biol. 310:442–53 [Google Scholar]
72. MacMahon H. 1948. Congenital alveolar dysplasia of the lungs. Am. J. Pathol. 24:919–31 [Google Scholar]
73. Mailleux AA, Tefft D, Ndiaye D, Itoh N, Thiery JP. et al. 2001. Evidence that SPROUTY2 functions as an inhibitor of mouse embryonic lung growth and morphogenesis. Mech. Dev. 102:81–94 [Google Scholar]
74. Malpel S, Mendelsohn C, Cardoso WV. 2000. Regulation of retinoic acid signaling during lung morphogenesis. Development 127:3057–67 [Google Scholar]
75. Marcet B, Chevalier B, Luxardi G, Coraux C, Zaragosi LE. et al. 2011. Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat. Cell Biol. 13:693–99 [Google Scholar]
76. Meenhuis A, van Veelen PA, de Looper H, van Boxtel N, van den Berge IJ. et al. 2011. MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1–regulated pathways in mice. Blood 118:916–25 [Google Scholar]
77. Metzger RJ, Klein OD, Martin GR, Krasnow MA. 2008. The branching programme of mouse lung development. Nature 453:745–50 [Google Scholar]
78. Min H, Danilenko DM, Scully SA, Bolon B, Ring BD. et al. 1998. Fgf-10 is required for both limb and lung development and exhibits striking functional similarity to Drosophila branchless. Genes Dev. 12:3156–61 [Google Scholar]
79. Morrisey EE, Hogan BLM. 2010. Preparing for the first breath: genetic and cellular mechanisms in lung development. Dev. Cell 18:8–23 [Google Scholar]
80. Morrisey EE, Tang Z, Sigrist K, Lu MM, Jiang F. et al. 1998. GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo. Genes Dev. 12:3579–90 [Google Scholar]
81. Motoyama J, Liu J, Mo R, Ding Q, Post M, Hui CC. 1998. Essential function of Gli2 and Gli3 in the formation of lung, trachea and oesophagus. Nat. Genet. 20:54–7 [Google Scholar]
82. Mou H, Zhao R, Sherwood R, Ahfeldt T, Lapey A. et al. 2012. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell 10:385–97 [Google Scholar]
83. Mucenski ML, Wert SE, Nation JM, Loudy DE, Huelsken J. et al. 2003. β-Catenin is required for specification of proximal/distal cell fate during lung morphogenesis. J. Biol. Chem. 278:40231–38 [Google Scholar]
84. Nora EP, Dekker J, Heard E. 2013. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?. BioEssays 35:818–28 [Google Scholar]
85. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. 2005. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435:839–43 [Google Scholar]
86. Okubo T, Hogan BL. 2004. Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm. J. Biol. 3:11 [Google Scholar]
87. Okubo T, Knoepfler PS, Eisenman RN, Hogan BL. 2005. Nmyc plays an essential role during lung development as a dosage-sensitive regulator of progenitor cell proliferation and differentiation. Development 132:1363–74 [Google Scholar]
88. Patel RM, Kandefer S, Walsh MC, Bell EF, Carlo WA. et al. 2015. Causes and timing of death in extremely premature infants from 2000 through 2011. N. Engl. J. Med. 372:331–40 [Google Scholar]
89. Peng T, Tian Y, Boogerd CJ, Lu MM, Kadzik RS. et al. 2013. Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor. Nature 500:589–92 [Google Scholar]
90. Pepicelli CV, Lewis PM, McMahon AP. 1998. Sonic hedgehog regulates branching morphogenesis in the mammalian lung. Curr. Biol. 8:1083–86 [Google Scholar]
91. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I. et al. 2010. Molecular maps of the reorganization of genome–nuclear lamina interactions during differentiation. Mol. Cell 38:603–13 [Google Scholar]
92. Perry SF, Wilson RJ, Straus C, Harris MB, Remmers JE. 2001. Which came first, the lung or the breath?. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 129:37–47 [Google Scholar]
93. Pilon M. 2014. Developmental genetics of the Caenorhabditis elegans pharynx. Wiley Interdiscip. Rev. Dev. Biol. 3:263–80 [Google Scholar]
94. Post LC, Ternet M, Hogan BL. 2000. Notch/Delta expression in the developing mouse lung. Mech. Dev. 98:95–98 [Google Scholar]
95. Que J, Luo X, Schwartz RJ, Hogan BL. 2009. Multiple roles for Sox2 in the developing and adult mouse trachea. Development 136:1899–907 [Google Scholar]
96. Rajagopal J, Carroll TJ, Guseh JS, Bores SA, Blank LJ. et al. 2008. Wnt7b stimulates embryonic lung growth by coordinately increasing the replication of epithelium and mesenchyme. Development 135:1625–34 [Google Scholar]
97. Rankin SA, Thi Tran H, Wlizla M, Mancini P, Shifley ET. et al. 2015. A molecular atlas of Xenopus respiratory system development. Dev. Dyn. 244:69–85 [Google Scholar]
98. Rawlins EL, Clark CP, Xue Y, Hogan BL. 2009. The Id2⁺ distal tip lung epithelium contains individual multipotent embryonic progenitor cells. Development 136:3741–45 [Google Scholar]
99. Rawlins EL, Ostrowski LE, Randell SH, Hogan BLM. 2007. Lung development and repair: contribution of the ciliated lineage. PNAS 104:410–17 [Google Scholar]
100. Sakai T, Larsen M, Yamada KM. 2003. Fibronectin requirement in branching morphogenesis. Nature 423:876–81 [Google Scholar]
101. Sakiyama J, Yamagishi A, Kuroiwa A. 2003. Tbx4-Fgf10 system controls lung bud formation during chicken embryonic development. Development 130:1225–34 [Google Scholar]
102. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF. et al. 2013. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife 2:e01749 [Google Scholar]
103. Schmidt LH, Spieker T, Koschmieder S, Schaffers S, Humberg J. et al. 2011. The long noncoding MALAT-1 RNA indicates a poor prognosis in non–small cell lung cancer and induces migration and tumor growth. J. Thorac. Oncol. 6:1984–92 [Google Scholar]
104. Sekine K, Ohuchi H, Fujiwara M, Yamasaki M, Yoshizawa T. et al. 1999. Fgf10 is essential for limb and lung formation. Nat. Genet. 21:138–41 [Google Scholar]
105. Sen P, Yang Y, Navarro C, Silva I, Szafranski P. et al. 2013. Novel FOXF1 mutations in sporadic and familial cases of alveolar capillary dysplasia with misaligned pulmonary veins imply a role for its DNA binding domain. Hum. Mutat. 34:801–11 [Google Scholar]
106. Serra R, Pelton RW, Moses HL. 1994. TGFβ1 inhibits branching morphogenesis and N-myc expression in lung bud organ cultures. Development 120:2153–61 [Google Scholar]
107. Shu W, Guttentag S, Wang Z, Andl T, Ballard P. et al. 2005. Wnt/β-catenin signaling acts upstream of N-myc, BMP4, and FGF signaling to regulate proximal-distal patterning in the lung. Dev. Biol. 283:226–39 [Google Scholar]
108. Shu W, Lu MM, Zhang Y, Tucker PW, Zhou D, Morrisey EE. 2007. Foxp2 and Foxp1 cooperatively regulate lung and esophagus development. Development 134:1991–2000 [Google Scholar]
109. Snitow ME, Li S, Morley MP, Rathi K, Lu MM. et al. 2015. Ezh2 represses the basal cell lineage during lung endoderm development. Development 142:108–17 [Google Scholar]
110. Sylvestre Y, De Guire V, Querido E, Mukhopadhyay UK, Bourdeau V. et al. 2007. An E2F/miR-20a autoregulatory feedback loop. J. Biol. Chem. 282:2135–43 [Google Scholar]
111. Szafranski P, Dharmadhikari AV, Brosens E, Gurha P, Kolodziejska KE. et al. 2013. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. Genome Res. 23:23–33 [Google Scholar]
112. Tang M, Xu W, Wang Q, Xiao W, Xu R. 2009. Potential of DNMT and its epigenetic regulation for lung cancer therapy. Curr. Genomics 10:336–52 [Google Scholar]
113. Tefft D, Lee M, Smith S, Crowe DL, Bellusci S, Warburton D. 2002. mSprouty2 inhibits FGF10-activated MAP kinase by differentially binding to upstream target proteins. Am. J. Physiol. Lung Cell. Mol. Physiol. 283:L700–6 [Google Scholar]
114. Tefft JD, Lee M, Smith S, Leinwand M, Zhao J. et al. 1999. Conserved function of mSpry-2, a murine homolog of Drosophila sprouty, which negatively modulates respiratory organogenesis. Curr. Biol. 9:219–22 [Google Scholar]
115. Tian Y, Zhang Y, Hurd L, Hannenhalli S, Liu F. et al. 2011. Regulation of lung endoderm progenitor cell behavior by miR302/367. Development 138:1235–45 [Google Scholar]
116. Tichelaar JW, Lim L, Costa RH, Whitsett JA. 1999. HNF-3/forkhead homologue-4 influences lung morphogenesis and respiratory epithelial cell differentiation in vivo. Dev. Biol. 213:405–17 [Google Scholar]
117. Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL. et al. 2014. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509:371–75 [Google Scholar]
118. Tsao PN, Chen F, Izvolsky KI, Walker J, Kukuruzinska MA. et al. 2008. γ-Secretase activation of Notch signaling regulates the balance of proximal and distal fates in progenitor cells of the developing lung. J. Biol. Chem. 283:29532–44 [Google Scholar]
119. Tsao PN, Vasconcelos M, Izvolsky KI, Qian J, Lu J, Cardoso WV. 2009. Notch signaling controls the balance of ciliated and secretory cell fates in developing airways. Development 136:2297–307 [Google Scholar]
120. Ulitsky I, Bartel DP. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46 [Google Scholar]
121. US Cancer Stat. Work. Group 2014. United States cancer statistics: 1999–2011. Incidence and mortality web-based report. Rep., US Dep. Health Hum. Serv., Cent. Dis. Control Prev., Natl. Cancer Inst., Atlanta
122. Vaucher YE, Peralta-Carcelen M, Finer NN, Carlo WA, Gantz MG. et al. 2012. Neurodevelopmental outcomes in the early CPAP and pulse oximetry trial. N. Engl. J. Med. 367:2495–504 [Google Scholar]
123. Ventura A, Young AG, Winslow MM, Lintault L, Meissner A. et al. 2008. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132:875–86 [Google Scholar]
124. Volpe MV, Chung E, Ulm JP, Gilchrist BF, Ralston S. et al. 2009. Aberrant cell adhesion molecule expression in human bronchopulmonary sequestration and congenital cystic adenomatoid malformation. Am. J. Physiol. Lung Cell. Mol. Physiol. 297:L143–52 [Google Scholar]
125. Wang P, Zhang W, Yang J, Qu J, Liu GH. 2012. Higher-order genomic organization in pluripotent stem cells. Protein Cell 3:483–86 [Google Scholar]
126. Wang Y, Huang C, Reddy Chintagari N, Bhaskaran M, Weng T. et al. 2013a. miR-375 regulates rat alveolar epithelial cell trans-differentiation by inhibiting Wnt/β-catenin pathway. Nucleic Acids Res. 41:3833–44 [Google Scholar]
127. Wang Y, Tian Y, Morley MP, Lu MM, Demayo FJ. et al. 2013b. Development and regeneration of Sox2⁺ endoderm progenitors are regulated by a Hdac1/2-Bmp4/Rb1 regulatory pathway.. Dev. Cell 24:345–58 [Google Scholar]
128. Wang Z, Dolle P, Cardoso WV, Niederreither K. 2006. Retinoic acid regulates morphogenesis and patterning of posterior foregut derivatives. Dev. Biol. 297:433–45 [Google Scholar]
129. Weaver M, Dunn NR, Hogan BL. 2000. Bmp4 and Fgf10 play opposing roles during lung bud morphogenesis. Development 127:2695–704 [Google Scholar]
130. Wei Z, Gao F, Kim S, Yang H, Lyu J. et al. 2013. Klf4 organizes long-range chromosomal interactions with the Oct4 locus in reprogramming and pluripotency. Cell Stem Cell 13:36–47 [Google Scholar]
131. Woods K, Thomson JM, Hammond SM. 2007. Direct regulation of an oncogenic micro-RNA cluster by E2F transcription factors. J. Biol. Chem. 282:2130–34 [Google Scholar]
132. Yates LL, Schnatwinkel C, Hazelwood L, Chessum L, Paudyal A. et al. 2013. Scribble is required for normal epithelial cell-cell contacts and lumen morphogenesis in the mammalian lung. Dev. Biol. 373:267–80 [Google Scholar]
133. Yates LL, Schnatwinkel C, Murdoch JN, Bogani D, Formstone CJ. et al. 2010. The PCP genes Celsr1 and Vangl2 are required for normal lung branching morphogenesis. Hum. Mol. Genet. 19:2251–67 [Google Scholar]
134. Yin Z, Gonzales L, Kolla V, Rath N, Zhang Y. et al. 2006. Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression. Am. J. Physiol. Lung Cell. Mol. Physiol. 291:L191–99 [Google Scholar]
135. Zhang B, Arun G, Mao YS, Lazar Z, Hung G. et al. 2012. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2:111–23 [Google Scholar]
136. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R. et al. 2013. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504:306–10 [Google Scholar]
137. Zhou L, Dey CR, Wert SE, Whitsett JA. 1996. Arrested lung morphogenesis in transgenic mice bearing an SP-C–TGF-β1 chimeric gene. Dev. Biol. 175:227–38 [Google Scholar]
138. Zhu L, Li H, Tang J, Zhu J, Zhang Y. 2012. Hyperoxia arrests alveolar development through suppression of histone deacetylases in neonatal rats. Pediatr. Pulmonol. 47:264–74 [Google Scholar]