Evolution, Expression, and Developmental Function of Hox-Embedded miRNAs

Current Topics in Developmental Biology

Volumn 99, Issue , 2012, Pages 31-57

  Mansfield, Jennifer H ^a   McGlinn, Edwina ^b  

^a Program on US Russia Relations at Columbia s Harriman Institute   (United States)

^b MONASH UNIVERSITY   (Australia)

Author keywords

Axial patterning; Homeotic; Hox; MicroRNA; Posterior prevalence

Indexed keywords

EID: 84857380270     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-387038-4.00002-1     Document Type: Chapter

References (119)

1. Aboobaker A.A., Blaxter M.L. Curr. Biol. 2003, 13:37-40.
2. Aboobaker A.A., Tomancak P., Patel N., Rubin G.M., Lai E.C. Proc. Natl. Acad. Sci. USA 2005, 102:18017-18022.
3. Amemiya C.T., Powers T.P., Prohaska S.J., Grimwood J., Schmutz J., Dickson M., Miyake T., Schoenborn M.A., Myers R.M., Ruddle F.H., Stadler P.F. Proc. Natl. Acad. Sci. USA 2010, 107:3622-3627.
4. Amores A., Force A., Yan Y.L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.L., Westerfield M., Ekker M., et al. Science 1998, 282:1711-1714.
5. Aravin A.A., Lagos-Quintana M., Yalcin A., Zavolan M., Marks D., Snyder B., Gaasterland T., Meyer J., Tuschl T. Dev. Cell 2003, 5:337-350.
6. Asli N.S., Kessel M. Dev. Biol. 2010, 344:857-868.
7. Bae E., Calhoun V.C., Levine M., Lewis E.B., Drewell R.A. Proc. Natl. Acad. Sci. USA 2002, 99:16847-16852.
8. Baek D., Villen J., Shin C., Camargo F.D., Gygi S.P., Bartel D.P. Nature 2008, 455:64-71.
9. Bartel D.P. Cell 2009, 136:215-233.
10. Bender W. Genes Dev. 2008, 22:14-19.
11. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. Nucleic Acids Res. 2004, 32:D23-D26.
12. Brend T., Gilthorpe J., Summerbell D., Rigby P.W. Development 2003, 130:2717-2728.
13. Brennecke J., Stark A., Russell R.B., Cohen S.M. PLoS Biol. 2005, 3:e85.
14. Brock H.W., Hodgson J.W., Petruk S., Mazo A. Biochem. Cell Biol. 2009, 87:27-34.
15. Butts T., Holland P.W., Ferrier D.E. Trends Genet. 2008, 24:259-262.
16. Campo-Paysaa F., Semon M., Cameron R.A., Peterson K.J., Schubert M. Evol. Dev. 2011, 13:15-27.
17. Carapuco M., Novoa A., Bobola N., Mallo M. Genes Dev. 2005, 19:2116-2121.
18. Carthew R.W., Sontheimer E.J. Cell 2009, 136:642-655.
19. Charite J., de Graaff W., Shen S., Deschamps J. Cell 1994, 78:589-601.
20. Chen F., Capecchi M.R. Dev. Biol. 1997, 181:186-196.
21. Chiang H.R., Schoenfeld L.W., Ruby J.G., Auyeung V.C., Spies N., Baek D., Johnston W.K., Russ C., Luo S., Babiarz J.E., Blelloch R., Schroth G.P., et al. Genes Dev. 2010, 24:992-1009.
22. Coulombe Y., Lemieux M., Moreau J., Aubin J., Joksimovic M., Berube-Simard F.A., Tabaries S., Boucherat O., Guillou F., Larochelle C., Tuggle C.K., Jeannotte L. PLoS One 2010, 5:e10600.
23. Cumberledge S., Zaratzian A., Sakonju S. Proc. Natl. Acad. Sci. USA 1990, 87:3259-3263.
24. Darnell D.K., Kaur S., Stanislaw S., Konieczka J.H., Yatskievych T.A., Antin P.B. Dev. Dyn. 2006, 235:3156-3165.
25. Deschamps J. Curr. Opin. Genet. Dev. 2007, 17:422-427.
26. Duboule D. Development 2007, 134:2549-2560.
27. Enright A.J., John B., Gaul U., Tuschl T., Sander C., Marks D.S. Genome Biol. 2003, 5:R1.
28. Fanarraga M.L., Charite J., Hage W.J., De Graaff W., Deschamps J. J. Neurosci. Methods 1997, 71:11-18.
29. Force A., Amores A., Postlethwait J.H. J. Exp. Zool. 2002, 294:30-46.
30. Fried C., Prohaska S.J., Stadler P.F. J. Exp. Zool. B Mol. Dev. Evol. 2003, 299:18-25.
31. Frobius A.C., Matus D.Q., Seaver E.C. PLoS One 2008, 3:e4004.
32. Gehring W.J., Kloter U., Suga H. Curr. Top. Dev. Biol. 2009, 88:35-61.
33. Gould A., Morrison A., Sproat G., White R.A., Krumlauf R. Genes Dev. 1997, 11:900-913.
34. Greer J.M., Capecchi M.R. Neuron 2002, 33:23-34.
35. Griffiths-Jones S. Nucleic Acids Res. 2004, 32:D109-D111.
36. Griffiths-Jones S., Hui J.H., Marco A., Ronshaugen M. EMBO Rep. 2011, 12:172-177.
37. Grimson A., Farh K.K., Johnston W.K., Garrett-Engele P., Lim L.P., Bartel D.P. Mol. Cell 2007, 27:91-105.
38. Guo H., Ingolia N.T., Weissman J.S., Bartel D.P. Nature 2010, 466:835-840.
39. Hadrys T., Prince V., Hunter M., Baker R., Rinkwitz S. J. Exp. Zool. B Mol. Dev. Evol. 2004, 302:147-164.
40. He X., Yan Y.L., DeLaurier A., Postlethwait J.H. Zebrafish 2011, 8:1-8.
41. He X., Yan Y.L., Eberhart J.K., Herpin A., Wagner T.U., Schartl M., Postlethwait J.H. Dev. Biol. 2011, 357:463-477.
42. Heimberg A.M., Cowper-Sal-lari R., Semon M., Donoghue P.C., Peterson K.J. Proc. Natl. Acad. Sci. USA 2010, 107:19379-19383.
43. Hendrix D., Levine M., Shi W. Genome Biol. 2010, 11:R39.
44. Herault Y., Fraudeau N., Zakany J., Duboule D. Development 1997, 124:3493-3500.
45. Holland P.W., Garcia-Fernandez J. Dev. Biol. 1996, 173:382-395.
46. Holstege J.C., de Graaff W., Hossaini M., Cano S.C., Jaarsma D., van den Akker E., Deschamps J. Proc. Natl. Acad. Sci. USA 2008, 105:6338-6343.
47. Horan G.S., Ramirez-Solis R., Featherstone M.S., Wolgemuth D.J., Bradley A., Behringer R.R. Genes Dev. 1995, 9:1667-1677.
48. Hornstein E., Shomron N. Nat. Genet. 2006, 38(Suppl.):S20-S24.
49. Hornstein E., Mansfield J.H., Yekta S., Hu J.K., Harfe B.D., McManus M.T., Baskerville S., Bartel D.P., Tabin C.J. Nature 2005, 438:671-674.
50. Huang H., Xie C., Sun X., Ritchie R.P., Zhang J., Chen Y.E. J. Biol. Chem. 2010, 285:9383-9389.
51. Huang Q.X., Cheng X.Y., Mao Z.C., Wang Y.S., Zhao L.L., Yan X., Ferris V.R., Xu R.M., Xie B.Y. PLoS One 2010, 5:e13271.
52. Ikuta T., Yoshida N., Satoh N., Saiga H. Proc. Natl. Acad. Sci. USA 2004, 101:15118-15123.
53. Kent W.J. Genome Res. 2002, 12:656-664.
54. Kessel M., Gruss P. Cell 1991, 67:89-104.
55. Kieny M., Mauger A., Sengel P. Dev. Biol. 1972, 28:142-161.
56. Kloosterman W.P., Wienholds E., de Bruijn E., Kauppinen S., Plasterk R.H. Nat. Methods 2006, 3:27-29.
57. Kmita M., Duboule D. Science 2003, 301:331-333.
58. Kondrashov N., Pusic A., Stumpf C.R., Shimizu K., Hsieh A.C., Xue S., Ishijima J., Shiroishi T., Barna M. Cell 2011, 145:383-397.
59. Kuroiwa A., Kloter U., Baumgartner P., Gehring W.J. EMBO J. 1985, 4:3757-3764.
60. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Science 2001, 294:853-858.
61. Lagos-Quintana M., Rauhut R., Meyer J., Borkhardt A., Tuschl T. RNA 2003, 9:175-179.
62. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A.O., Landthaler M., Lin C., Socci N.D., et al. Cell 2007, 129:1401-1414.
63. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. Science 2001, 294:858-862.
64. Lemons D., McGinnis W. Science 2006, 313:1918-1922.
65. Lewis E.B. Am. Zool. 1963, 3:33-56.
66. Lewis E.B. Nature 1978, 276:565-570.
67. Lewis E.B. Int. J. Dev. Biol. 1998, 42:403-415.
68. Li X., Cassidy J.J., Reinke C.A., Fischboeck S., Carthew R.W. Cell 2009, 137:273-282.
69. Lim L.P., Glasner M.E., Yekta S., Burge C.B., Bartel D.P. Science 2003, 299:1540.
70. Lim L.P., Lau N.C., Garrett-Engele P., Grimson A., Schelter J.M., Castle J., Bartel D.P., Linsley P.S., Johnson J.M. Nature 2005, 433:769-773.
71. Mainguy G., Koster J., Woltering J., Jansen H., Durston A. PLoS One 2007, 2:e356.
72. Mansfield J.H., Harfe B.D., Nissen R., Obenauer J., Srineel J., Chaudhuri A., Farzan-Kashani R., Zuker M., Pasquinelli A.E., Ruvkun G., Sharp P.A., Tabin C.J., et al. Nat. Genet. 2004, 36:1079-1083.
73. Marco A., Hui J.H., Ronshaugen M., Griffiths-Jones S. Genome Biol. Evol. 2010, 2:686-696.
74. McGinnis W., Krumlauf R. Cell 1992, 68:283-302.
75. McGlinn E., Yekta S., Mansfield J.H., Soutschek J., Bartel D.P., Tabin C.J. Proc. Natl. Acad. Sci. USA 2009, 106:18610-18615.
76. McIntyre D.C., Rakshit S., Yallowitz A.R., Loken L., Jeannotte L., Capecchi M.R., Wellik D.M. Development 2007, 134:2981-2989.
77. Mineno J., Okamoto S., Ando T., Sato M., Chono H., Izu H., Takayama M., Asada K., Mirochnitchenko O., Inouye M., Kato I. Nucleic Acids Res. 2006, 34:1765-1771.
78. Miura S., Nozawa M., Nei M. Genome Biol. Evol. 2011, 3:129-139.
79. Nelson C.E., Morgan B.A., Burke A.C., Laufer E., DiMambro E., Murtaugh L.C., Gonzales E., Tessarollo L., Parada L.F., Tabin C. Development 1996, 122:1449-1466.
80. Ohtsuki S., Levine M., Cai H.N. Genes Dev. 1998, 12:547-556.
81. Prohaska S.J., Stadler P.F. Theory Biosci. 2004, 123:89-110.
82. Qian J., Zhang Z., Liang J., Ge Q., Duan X., Ma F., Li F. Genomics 2011, 97:294-303.
83. Qiu R., Liu Y., Wu J.Y., Liu K., Mo W., He R. Brain Res. Bull. 2009, 79:26-31.
84. Rathjen T., Pais H., Sweetman D., Moulton V., Munsterberg A., Dalmay T. FEBS Lett. 2009, 583:1422-1426.
85. Ravi V., Lam K., Tay B.H., Tay A., Brenner S., Venkatesh B. Proc. Natl. Acad. Sci. USA 2009, 106:16327-16332.
86. Richardson M.K., Crooijmans R.P., Groenen M.A. Cytogenet. Genome Res. 2007, 117:110-119.
87. Riley P.D., Carroll S.B., Scott M.P. Genes Dev. 1987, 1:716-730.
88. Rinn J.L., Kertesz M., Wang J.K., Squazzo S.L., Xu X., Brugmann S.A., Goodnough L.H., Helms J.A., Farnham P.J., Segal E., Chang H.Y. Cell 2007, 129:1311-1323.
89. Ronshaugen M., Biemar F., Piel J., Levine M., Lai E.C. Genes Dev. 2005, 19:2947-2952.
90. Ruby J.G., Stark A., Johnston W.K., Kellis M., Bartel D.P., Lai E.C. Genome Res. 2007, 17:1850-1864.
91. Sehm T., Sachse C., Frenzel C., Echeverri K. Dev. Biol. 2009, 334:468-480.
92. Sharpe J., Nonchev S., Gould A., Whiting J., Krumlauf R. EMBO J. 1998, 17:1788-1798.
93. Sperling E.A., Vinther J., Moy V.N., Wheeler B.M., Semon M., Briggs D.E., Peterson K.J. Proc. R. Soc. B 2009, 276:4315-4322.
94. Stadler P.F., Fried C., Prohaska S.J., Bailey W.J., Misof B.Y., Ruddle F.H., Wagner G.P. Mol. Phylogenet. Evol. 2004, 32:686-694.
95. Stark A., Brennecke J., Russell R.B., Cohen S.M. PLoS Biol. 2003, 1:E60.
96. Stark A., Kheradpour P., Parts L., Brennecke J., Hodges E., Hannon G.J., Kellis M. Genome Res. 2007, 17:1865-1879.
97. Stark A., Bushati N., Jan C.H., Kheradpour P., Hodges E., Brennecke J., Bartel D.P., Cohen S.M., Kellis M. Genes Dev. 2008, 22:8-13.
98. Staton A.A., Knaut H., Giraldez A.J. Nat. Genet. 2011, 43:204-211.
99. Stratford T., Logan C., Zile M., Maden M. Mech. Dev. 1999, 81:115-125.
100. Takacs C.M., Giraldez A.J. Semin. Cell Dev. Biol. 2011, 21:760-767.
101. Tang G.Q., Maxwell E.S. Genome Res. 2008, 18:104-112.
102. Tanzer A., Amemiya C.T., Kim C.B., Stadler P.F. J. Exp. Zool. B Mol. Dev. Evol. 2005, 304:75-85.
103. Thomsen S., Azzam G., Kaschula R., Williams L.S., Alonso C.R. Development 2010, 137:2951-2960.
104. Tyler D.M., Okamura K., Chung W.J., Hagen J.W., Berezikov E., Hannon G.J., Lai E.C. Genes Dev. 2008, 22:26-36.
105. van den Akker E., Reijnen M., Korving J., Brouwer A., Meijlink F., Deschamps J. Mech. Dev. 1999, 89:103-114.
106. van den Akker E., Fromental-Ramain C., de Graaff W., Le Mouellic H., Brulet P., Chambon P., Deschamps J. Development 2001, 128:1911-1921.
107. van Rooij E., Sutherland L.B., Qi X., Richardson J.A., Hill J., Olson E.N. Science 2007, 316:575-579.
108. Wang K.C., Yang Y.W., Liu B., Sanyal A., Corces-Zimmerman R., Chen Y., Lajoie B.R., Protacio A., Flynn R.A., Gupta R.A., Wysocka J., Lei M., et al. Nature 2011, 472:120-124.
109. Wellik D.M. Dev. Dyn. 2007, 236:2454-2463.
110. Wellik D.M. Curr. Top. Dev. Biol. 2009, 88:257-278.
111. Wellik D.M., Capecchi M.R. Science 2003, 301:363-367.
112. Wheeler B.M., Heimberg A.M., Moy V.N., Sperling E.A., Holstein T.W., Heber S., Peterson K.J. Evol. Dev. 2009, 11:50-68.
113. Wienholds E., Kloosterman W.P., Miska E., Alvarez-Saavedra E., Berezikov E., de Bruijn E., Horvitz H.R., Kauppinen S., Plasterk R.H. Science 2005, 309:310-311.
114. Woltering J.M., Durston A.J. Nat. Genet. 2006, 38:601-602.
115. Woltering J.M., Durston A.J. PLoS One 2008, 3:e1396.
116. Yekta S., Shih I.H., Bartel D.P. Science 2004, 304:594-596.
117. Yekta S., Tabin C.J., Bartel D.P. Nat. Rev. Genet. 2008, 9:789-796.
118. Zhao Z., Boyle T.J., Liu Z., Murray J.I., Wood W.B., Waterston R.H. PLoS Genet. 2010, 6:e1001089.
119. Zhou J., Ashe H., Burks C., Levine M. Development 1999, 126:3057-3065.