Exploiting Drosophila Genetics to Understand MicroRNA Function and Regulation

Current Topics in Developmental Biology

Volumn 99, Issue , 2012, Pages 201-235

  Dai, Qi ^a   Smibert, Peter ^a   Lai, Eric C ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

Drosophila; EP element; Epistasis; Gal4 UAS system; Knockout; MicroRNA; Sensor; Sponge

Indexed keywords

EID: 84857412362     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-387038-4.00008-2     Document Type: Chapter

References (150)

1. Abbott A.L., Alvarez-Saavedra E., Miska E.A., Lau N.C., Bartel D.P., Horvitz H.R., Ambros V. Dev. Cell 2005, 9:403-414.
2. Abdelilah-Seyfried S., Chan Y.M., Zeng C., Justice N.J., Younger-Shepherd S., Sharp L.E., et al. Genetics 2000, 155:733-752.
3. Aboobaker A.A., Tomancak P., Patel N., Rubin G.M., Lai E.C. Proc. Natl. Acad. Sci. USA 2005, 102:18017-18022.
4. Affolter M., Basler K. Nat. Rev. Genet. 2007, 8:663-674.
5. Alarcon C., Zaromytidou A.I., Xi Q., Gao S., Yu J., Fujisawa S., et al. Cell 2009, 139:757-769.
6. Alvarez-Saavedra E., Horvitz H.R. Curr. Biol. 2010, 20:367-373.
7. Ambros V., Lee R.C., Lavanway A., Williams P.T., Jewell D. Curr. Biol. 2003, 13:807-818.
8. Aravin A., Lagos-Quintana M., Yalcin A., Zavolan M., Marks D., Snyder B., et al. Dev. Cell 2003, 5:337-350.
9. Baek D., Villen J., Shin C., Camargo F.D., Gygi S.P., Bartel D.P. Nature 2008, 455:64-71.
10. Bartel D.P. Cell 2009, 136:215-233.
11. Bejarano F., Smibert P., Lai E.C. Dev. Biol. 2010, 338:63-73.
12. Bellen H.J., Levis R.W., Liao G., He Y., Carlson J.W., Tsang G., et al. Genetics 2004, 167:761-781.
13. Bellen H.J., Levis R.W., He Y., Carlson J.W., Evans-Holm M., Bae E., et al. Genetics 2011, 188:731-743.
14. Bender W. Genes Dev. 2008, 22:14-19.
15. Berezikov E., Robine N., Samsonova A., Westholm J.O., Naqvi A., Hung J.H., et al. Genome Res. 2011, 21:203-215.
16. Biemar F., Zinzen R., Ronshaugen M., Sementchenko V., Manak J.R., Levine M.S. Proc. Natl. Acad. Sci. USA 2005, 102:15907-15911.
17. Bier E., Väessin H., Shepherd S., Lee K., McCall K., Barbel S., et al. Genes Dev. 1989, 3:1273-1287.
18. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., et al. Nature 2007, 447:799-816.
19. Biryukova I., Asmar J., Abdesselem H., Heitzler P. Dev. Biol. 2009, 327:487-496.
20. Brand A.H., Perrimon N. Development 1993, 118:401-415.
21. Brennecke J., Hipfner D.R., Stark A., Russell R.B., Cohen S.M. Cell 2003, 113:25-36.
22. Brennecke J., Stark A., Russell R.B., Cohen S.M. PLoS Biol. 2005, 3:e85.
23. Brenner J.L., Jasiewicz K.L., Fahley A.F., Kemp B.J., Abbott A.L. Curr. Biol. 2010, 20:1321-1325.
24. Brodersen P., Voinnet O. Nat. Rev. Mol. Cell Biol. 2009, 10:141-148.
25. Bushati N., Stark A., Brennecke J., Cohen S.M. Curr. Biol. 2008, 18:501-506.
26. Caygill E.E., Johnston L.A. Curr. Biol. 2008, 18:943-950.
27. Cayirlioglu P., Kadow I.G., Zhan X., Okamura K., Suh G.S., Gunning D., et al. Science 2008, 319:1256-1260.
28. Chalfie M., Horvitz H.R., Sulston J.E. Cell 1981, 24:59-69.
29. Choi C.M., Vilain S., Langen M., Van Kelst S., De Geest N., Yan J., et al. Science 2009, 324:54.
30. Chung W.J., Agius P., Westholm J.O., Chen M., Okamura K., Robine N., et al. Genome Res. 2011, 21:286-300.
31. Czech B., Hannon G.J. Nat. Rev. Genet. 2010, 12:19-31.
32. Deak P., Omar M.M., Saunders R.D., Pal M., Komonyi O., Szidonya J., et al. Genetics 1997, 147:1697-1722.
33. Dietzl G., Chen D., Schnorrer F., Su K.C., Barinova Y., Fellner M., et al. Nature 2007, 448:151-156.
34. Doench J.G., Sharp P.A. Genes Dev. 2004, 18:504-511.
35. Ebert M.S., Neilson J.R., Sharp P.A. Nat. Methods 2007, 4:721-726.
36. Ejsmont R.K., Sarov M., Winkler S., Lipinski K.A., Tomancak P. Nat. Methods 2009, 6:435-437.
37. Enderle D., Beisel C., Stadler M.B., Gerstung M., Athri P., Paro R. Genome Res. 2011, 21:216-226.
38. Ferrigno O., Lallemand F., Verrecchia F., L'Hoste S., Camonis J., Atfi A., Mauviel A. Oncogene 2002, 21:4879-4884.
39. Flynt A.S., Lai E.C. Nat. Rev. Genet. 2008, 9:831-842.
40. Flynt A.S., Chung W.J., Greimann J.C., Lima C.D., Lai E.C. Mol. Cell 2010, 38:900-907.
41. Friedman R.C., Farh K.K., Burge C.B., Bartel D.P. Genome Res. 2009, 19:92-105.
42. Friggi-Grelin F., Lavenant-Staccini L., Therond P. Genetics 2008, 179:429-439.
43. Gao G., McMahon C., Chen J., Rong Y.S. Proc. Natl. Acad. Sci. USA 2008, 105:13999-14004.
44. Gentner B., Schira G., Giustacchini A., Amendola M., Brown B.D., Ponzoni M., Naldini L. Nat. Methods 2009, 6:63-66.
45. Gerstein M.B., Lu Z.J., Van Nostrand E.L., Cheng C., Arshinoff B.I., Liu T., et al. Science 2010, 330:1775-1787.
46. Gong W.J., Golic K.G. Proc. Natl. Acad. Sci. USA 2003, 100:2556-2561.
47. Graveley B.R., Brooks A.N., Carlson J.W., Duff M.O., Landolin J.M., Yang L., et al. Nature 2011, 471:473-479.
48. Guo H., Ingolia N.T., Weissman J.S., Bartel D.P. Nature 2010, 466:835-840.
49. Hagen J.W., Lai E.C. Cell Cycle 2008, 7:2327-2332.
50. Hardiman K.E., Brewster R., Khan S.M., Deo M., Bodmer R. Genetics 2002, 161:231-247.
51. He Q., Bardet A.F., Patton B., Purvis J., Johnston J., Paulson A., et al. Nat. Genet. 2011, 43:414-420.
52. Herranz H., Perez L., Martin F.A., Milan M. EMBO J. 2008, 27:1633-1645.
53. Hilgers V., Bushati N., Cohen S.M. PLoS Biol. 2010, 8:e1000396.
54. Hipfner D.R., Weigmann K., Cohen S.M. Genetics 2002, 161:1527-1537.
55. Huang J., Zhou W., Dong W., Watson A.M., Hong Y. Proc. Natl. Acad. Sci. USA 2009, 106:8284-8289.
56. Hyun S., Lee J.H., Jin H., Nam J., Namkoong B., Lee G., et al. Cell 2009, 139:1096-1108.
57. Iovino N., Pane A., Gaul U. Dev. Cell 2009, 17:123-133.
58. Jan C.H., Friedman R.C., Ruby J.G., Bartel D.P. Nature 2010, 469:97-101.
59. Johnston R.J., Hobert O. Nature 2003, 426:845-849.
60. Kadener S., Menet J.S., Sugino K., Horwich M.D., Weissbein U., Nawathean P., et al. Genes Dev. 2009, 23:2179-2191.
61. Kadener S., Rodriguez J., Abruzzi K.C., Khodor Y.L., Sugino K., Marr M.T., et al. RNA 2009, 15:537-545.
62. Karim F.D., Chang H.C., Therrien M., Wassarman D.A., Laverty T., Rubin G.M. Genetics 1996, 143:315-329.
63. Karr J., Vagin V., Chen K., Ganesan S., Olenkina O., Gvozdev V., Featherstone D.E. J. Cell Biol. 2009, 185:685-697.
64. Karres J.S., Hilgers V., Carrera I., Treisman J., Cohen S.M. Cell 2007, 131:136-145.
65. Kennerdell J.R., Carthew R.W. Nat. Biotechnol. 2000, 18:896-898.
66. Kim V.N., Han J., Siomi M.C. Nat. Rev. Mol. Cell Biol. 2009, 10:126-139.
67. Kim Y.K., Heo I., Kim V.N. Cell 2010, 143:703-709.
68. King I.N., Qian L., Liang J., Huang Y., Shieh J.T., Kwon C., Srivastava D. Dev. Cell 2011, 20:497-510.
69. Klämbt C., Knust E., Tietze K., Campos-Ortega J. EMBO J. 1989, 8:203-210.
70. Kosman D., Mizutani C.M., Lemons D., Cox W.G., McGinnis W., Bier E. Science 2004, 305:846.
71. Kraut R., Menon K., Zinn K. Curr. Biol. 2001, 11:417-430.
72. Krutzfeldt J., Rajewsky N., Braich R., Rajeev K.G., Tuschl T., Manoharan M., Stoffel M. Nature 2005, 438:685-689.
73. Kwon C., Han Z., Olson E.N., Srivastava D. Proc. Natl. Acad. Sci. USA 2005, 102:18986-18991.
74. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Science 2001, 294:853-858.
75. Lai E.C. Nat. Genet. 2002, 30:363-364.
76. Lai E.C., Posakony J.W. Development 1997, 124:4847-4856.
77. Lai E.C., Posakony J.W. Cell 1998, 93:1103-1104.
78. Lai E.C., Burks C., Posakony J.W. Development 1998, 125:4077-4088.
79. Lai E.C., Tomancak P., Williams R.W., Rubin G.M. Genome Biol. 2003, 4:R42.1-R42.20.
80. Lai E.C., Tam B., Rubin G.M. Genes Dev. 2005, 19:1067-1080.
81. Leaman D., Chen P.Y., Fak J., Yalcin A., Pearce M., Unnerstall U., et al. Cell 2005, 121:1097-1108.
82. Lee R.C., Feinbaum R.L., Ambros V. Cell 1993, 75:843-854.
83. Lee Y., Kim M., Han J., Yeom K.H., Lee S., Baek S.H., Kim V.N. EMBO J. 2004, 23:4051-4060.
84. Lee Y., Lee J., Bang S., Hyun S., Kang J., Hong S.T., et al. Nat. Genet. 2005, 37:305-310.
85. Leviten M.W., Lai E.C., Posakony J.W. Development 1997, 124:4039-4051.
86. Lewis E.B. Nature 1978, 276:565-570.
87. Li X., Carthew R.W. Cell 2005, 123:1267-1277.
88. Li Y., Wang F., Lee J.A., Gao F.B. Genes Dev. 2006, 20:2793-2805.
89. Li X., Cassidy J.J., Reinke C.A., Fischboeck S., Carthew R.W. Cell 2009, 137:273-282.
90. Lifschytz E., Green M.M. Mol. Gen. Genet. 1979, 171:153-159.
91. Lim L.P., Lau N.C., Garrett-Engele P., Grimson A., Schelter J.M., Castle J., et al. Nature 2005, 433:769-773.
92. Lindsley D.L., Sandler L., Baker B.S., Carpenter A.T.C., Denell R.F., Hall J.C., et al. Genetics 1972, 71:157-184.
93. Loya C.M., Lu C.S., Van Vactor D., Fulga T.A. Nat. Methods 2009, 6:897-903.
94. Macquarrie K.L., Fong A.P., Morse R.H., Tapscott S.J. Trends Genet. 2011, 27:141-148.
95. Manak J.R., Dike S., Sementchenko V., Kapranov P., Biemar F., Long J., et al. Nat. Genet. 2006, 38:1151-1158.
96. Mangone M., Manoharan A.P., Thierry-Mieg D., Thierry-Mieg J., Han T., Mackowiak S.D., et al. Science 2010, 329:432-435.
97. Martin F.A., Perez-Garijo A., Moreno E., Morata G. Development 2004, 131:4921-4930.
98. Miska E.A., Alvarez-Saavedra E., Abbott A.L., Lau N.C., Hellman A.B., McGonagle S.M., et al. PLoS Genet. 2007, 3:e215.
99. Moss E.G., Lee R.C., Ambros V. Cell 1997, 88:637-646.
100. Nairz K., Rottig C., Rintelen F., Zdobnov E., Moser M., Hafen E. Dev. Biol. 2006, 291:314-324.
101. Nolo R., Abbott L., Bellen H.J. Genetics 2001, 157:307-315.
102. Nolo R., Morrison C.M., Tao C., Zhang X., Halder G. Curr. Biol. 2006, 16:1895-1904.
103. Oh H., Irvine K.D. Dev. Cell 2011, 20:109-122.
104. Okamura K., Hagen J.W., Duan H., Tyler D.M., Lai E.C. Cell 2007, 130:89-100.
105. O'Keefe L.V., Smibert P., Colella A., Chataway T.K., Saint R., Richards R.I. Trends Genet. 2007, 23:238-242.
106. Pan D. Dev. Cell 2010, 19:491-505.
107. Parks A.L., Cook K.R., Belvin M., Dompe N.A., Fawcett R., Huppert K., et al. Nat. Genet. 2004, 36:288-292.
108. Parrish J.Z., Xu P., Kim C.C., Jan L.Y., Jan Y.N. Neuron 2009, 63:788-802.
109. Pena-Rangel M.T., Rodriguez I., Riesgo-Escovar J.R. Genetics 2002, 160:1035-1050.
110. Peng H.W., Slattery M., Mann R.S. Genes Dev. 2009, 23:2307-2319.
111. Raisin S., Pantalacci S., Breittmayer J.P., Leopold P. Genetics 2003, 164:1015-1025.
112. Reinhart B.J., Slack F., Basson M., Pasquinelli A., Bettinger J., Rougvie A., et al. Nature 2000, 403:901-906.
113. Roegiers F., Kavaler J., Tolwinski N., Chou Y.T., Duan H., Bejarano F., et al. Genetics 2009, 182:407-410.
114. Rong Y.S., Golic K.G. Science 2000, 288:2013-2018.
115. Rong Y.S., Golic K.G. Genetics 2001, 157:1307-1312.
116. Rong Y.S., Titen S.W., Xie H.B., Golic M.M., Bastiani M., Bandyopadhyay P., et al. Genes Dev. 2002, 16:1568-1581.
117. Ronshaugen M., Biemar F., Piel J., Levine M., Lai E.C. Genes Dev. 2005, 19:2947-2952.
118. Rørth P., Szabo K., Bailey A., Laverty T., Rehm J., Rubin G.M., et al. Development 1998, 125:1049-1057.
119. Roy S., Ernst J., Kharchenko P.V., Kheradpour P., Negre N., Eaton M.L., et al. Science 2010, 330:1787-1797.
120. Ruby J.G., Jan C.H., Bartel D.P. Nature 2007, 448:83-86.
121. Ruby J.G., Stark A., Johnston W.K., Kellis M., Bartel D.P., Lai E.C. Genome Res. 2007, 17:1850-1864.
122. Ruvkun G., Giusto J. Nature 1989, 338:313-319.
123. Ryder E., Ashburner M., Bautista-Llacer R., Drummond J., Webster J., Johnson G., et al. Genetics 2007, 177:615-629.
124. Silver S.J., Hagen J.W., Okamura K., Perrimon N., Lai E.C. Proc. Natl. Acad. Sci. USA 2007, 104:18151-18156.
125. Simon M.A., Bowtell D.D., Dodson G.S., Laverty T.R., Rubin G.M. Cell 1991, 67:701-716.
126. Siomi H., Siomi M.C. Mol. Cell 2010, 38:323-332.
127. Smibert P., Lai E.C. Cell Cycle 2008, 7:2500-2508.
128. Smibert P., Lai E.C. Semin. Cell Dev. Biol. 2010, 21:745-753.
129. Sokol N.S., Ambros V. Genes Dev. 2005, 19:2343-2354.
130. Sokol N.S., Xu P., Jan Y.N., Ambros V. Genes Dev. 2008, 22:1591-1596.
131. Spradling A.C., Stern D., Beaton A., Rhem E.J., Laverty T., Mozden N., et al. Genetics 1999, 153:135-177.
132. Stark A., Brennecke J., Russell R.B., Cohen S.M. PLoS Biol. 2003, 1:E60.
133. Stark A., Brennecke J., Bushati N., Russell R.B., Cohen S.M. Cell 2005, 123:1133-1146.
134. Stark A., Lin M.F., Kheradpour P., Pedersen J.S., Parts L., Carlson J.W., et al. Nature 2007, 450:219-232.
135. Stark A., Bushati N., Jan C.H., Kheradpour P., Hodges E., Brennecke J., et al. Genes Dev. 2008, 22:8-13.
136. Teleman A.A., Maitra S., Cohen S.M. Genes Dev. 2006, 20:417-422.
137. Thibault S.T., Singer M.A., Miyazaki W.Y., Milash B., Dompe N.A., Singh C.M., et al. Nat. Genet. 2004, 36:283-287.
138. Thompson B.J., Cohen S.M. Cell 2006, 126:767-774.
139. Tsurudome K., Tsang K., Liao E.H., Ball R., Penney J., Yang J.S., et al. Neuron 2010, 68:879-893.
140. 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.
141. Varghese J., Cohen S.M. Genes Dev. 2007, 21:2277-2282.
142. Varghese J., Lim S.F., Cohen S.M. Genes Dev. 2010, 24:2748-2753.
143. Venken K.J., Carlson J.W., Schulze K.L., Pan H., He Y., Spokony R., et al. Nat. Methods 2009, 6:431-434.
144. Weng R., Chen Y.W., Bushati N., Cliffe A., Cohen S.M. Genetics 2009, 183:399-402.
145. Wightman B., Burglin T.R., Gatto J., Arasu P., Ruvkun G. Genes Dev. 1991, 5:1813-1824.
146. Wightman B., Ha I., Ruvkun G. Cell 1993, 75:855-862.
147. Xu P., Vernooy S.Y., Guo M., Hay B.A. Curr. Biol. 2003, 13:790-795.
148. Xu X.L., Li Y., Wang F., Gao F.B. J. Neurosci. 2008, 28:11883-11889.
149. Yang J.S., Lai E.C. Mol. Cell 2011, 43:892-903.
150. Yang Y., Xu S., Xia L., Wang J., Wen S., Jin P., Chen D. PLoS Genet. 2009, 5:e1000444.