Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo

Chaos

Volumn 23, Issue 2, 2013, Pages

  Kim, Yoosik ^a   Iagovitina, Antonina ^a,b   Ishihara, Keisuke ^a   Fitzgerald, Kate M ^a   Deplancke, Bart ^b   Papatsenko, Dmitri ^c   Shvartsman, Stanislav Y ^a  

^a Princeton University   (United States)

^b EPFL   (Switzerland)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; REPRESSOR PROTEIN;

ANIMAL; ANIMAL EMBRYO; ARTICLE; BIOLOGICAL MODEL; DROSOPHILA MELANOGASTER; ENHANCER REGION; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PRENATAL DEVELOPMENT; SIGNAL TRANSDUCTION; EMBRYOLOGY;

ANIMALS; BASE SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EMBRYO, NONMAMMALIAN; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MAP KINASE SIGNALING SYSTEM; MITOGEN-ACTIVATED PROTEIN KINASES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84880369254     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4808157     Document Type: Article

References (56)

1. Halfon M.S. Carmena A.M. Gisselbrecht S. Sackerson C.M. Jimenez F. Baylies M.K. Michelson A.M. Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. Cell 2000, 103(1):63-74. 10.1016/S0092-8674(00)00105-7, and ",".
2. Elstob P.R. Brodu V. Gould A.P. Spalt-dependent switching between two cell fates that are induced by the Drosophila EGF receptor. Development 2001, 128(5):723-732. and ",".
3. Nakakuki T. Birtwistle M.R. Saeki Y. Yumoto N. Ide K. Nagashima T. Brusch L. Ogunnaike B.A. Okada-Hatakeyama M. Kholodenko B.N. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 2010, 141(5):884-896. 10.1016/j.cell.2010.03.054, and ",".
4. Guardavaccaro D. Clevers H. Wnt/beta-Catenin and MAPK signaling: Allies and enemies in different battlefields. Sci. Signal. 2012, 5(219):pe15. 10.1126/scisignal.2002921, and ",".
5. Simon M.A. Receptor tyrosine kinases: Specific outcomes from general signals. Cell 2000, 103(1):13-15. 10.1016/S0092-8674(00)00100-8, ",".
6. Sundaram M.V. The love-hate relationship between Ras and Notch. Genes Dev. 2005, 19(16):1825-1839. 10.1101/gad.1330605, ",".
7. Li W.X. Functions and mechanisms of receptor tyrosine kinase Torso signaling: Lessons from Drosophila embryonic terminal development. Dev. Dyn. 2005, 232(3):656-672. 10.1002/dvdy.20295, ",".
8. Furriols M. Casanova J. In and out of Torso RTK signalling. EMBO J. 2003, 22(9):1947-1952. 10.1093/emboj/cdg224, and ",".
9. Jimenez G. Guichet A. Ephrussi A. Casanova J. Relief of gene repression by torso RTK signaling: Role of capicua in Drosophila terminal and dorsoventral patterning. Genes Dev. 2000, 14(2):224-231. 10.1101/gad.14.2.224, and ",".
10. Grimm O. Sanchez Zini V. Kim Y. Casanova J. Shvartsman S.Y. Wieschaus E. Torso RTK controls Capicua degradation by changing its subcellular localization. Development 2012, 139(21):3962-3968. 10.1242/dev.084327, and ",".
11. Löhr U. Chung H.-R. Beller M. Jäckle H. Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(51):21695-21700. 10.1073/pnas.0910225106, and ",".
12. Porcher A. Dostatni N. The Bicoid morphogen system. Curr. Biol. 2010, 20(5):R249-R254. 10.1016/j.cub.2010.01.026, and ",".
13. Pignoni F. Steingrimsson E. Lengyel J.A. Bicoid and the terminal system activate tailless expression in the early Drosophila embryo. Development 1992, 115(1):239-251. and ",".
14. Löhr U. Chung H.R. Beller M. Jäckle H. Bicoid: Morphogen function revisited. Fly (Austin) 2010, 4(3):236-240. 10.4161/fly.4.3.11862, and ",".
15. Driever W. Ma J. Nusslein-Volhard C. Ptashne M. Rescue of bicoid mutant Drosophila embryos by bicoid fusion proteins containing heterologous activating sequences. Nature 1989, 342(6246):149-154. 10.1038/342149a0, and ",".
16. Schupbach T. Wieschaus E. Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations. Genetics 1989, 121(1):101-117. and ",".
17. Konrad K.D. Goralski T.J. Mahowald A.P. Developmental genetics of the gastrulation defective locus in Drosophila melanogaster. Dev. Biol. 1988, 127(1):133-142. 10.1016/0012-1606(88)90195-9, and ",".
18. Stathopoulos A. Van Drenth M. Erives A. Markstein M. Levine M. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 2002, 111(5):687-701. 10.1016/S0092-8674(02)01087-5, and ",".
19. Goldstein R.E. Jimenez G. Cook O. Gur D. Paroush Z. Huckebein repressor activity in Drosophila terminal patterning is mediated by Groucho. Development 1999, 126(17):3747-3755. and ",".
20. Struffi P. Arnosti D.N. Functional interaction between the Drosophila knirps short range transcriptional repressor and RPD3 histone deacetylase. J. Biol. Chem. 2005, 280(49):40757-40765. 10.1074/jbc.M506819200, and ",".
21. Ashyraliyev M. Siggens K. Janssens H. Blom J. Akam M. Jaeger J. Gene circuit analysis of the terminal gap gene huckebein. PLOS Comput. Biol. 2009, 5(10):e1000548. 10.1371/journal.pcbi.1000548, and ",".
22. Coppey M. Boettiger A.N. Berezhkovskii A.M. Shvartsman S.Y. Nuclear trapping shapes the terminal gradient in the Drosophila embryo. Curr. Biol. 2008, 18(12):915-919. 10.1016/j.cub.2008.05.034, and ",".
23. Chung K. Kim Y. Kanodia J.S. Gong E. Shvartsman S.Y. Lu H. A microfluidic array for large-scale ordering and orientation of embryos. Nat. Methods 2011, 8(2):171-176. 10.1038/nmeth.1548, and ",".
24. Coppey M. Berezhkovskii A.M. Kim Y. Boettiger A.N. Shvartsman S.Y. Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein. Dev. Biol. 2007, 312(2):623-630. 10.1016/j.ydbio.2007.09.058, and ",".
25. Kanodia J.S. Rikhy R. Kim Y. Lund V.K. DeLotto R. Lippincott-Schwartz J. Shvartsman S.Y. Dynamics of the Dorsal morphogen gradient. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(51):21707-21712. 10.1073/pnas.0912395106, and ",".
26. Kim Y. Andreu M.J. Lim B. Chung K. Terayama M. Jimenez G. Berg C.A. Lu H. Shvartsman S.Y. Gene regulation by MAPK substrate competition. Dev. Cell 2011, 20(6):880-887. 10.1016/j.devcel.2011.05.009, and ",".
27. Kim Y. Coppey M. Grossman R. Ajuria L. Jimenez G. Paroush Z. Shvartsman S.Y. MAPK substrate competition integrates patterning signals in the Drosophila embryo. Curr. Biol. 2010, 20(5):446-451. 10.1016/j.cub.2010.01.019, and ",".
28. Driever W. Nusslein-Volhard C. The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell 1988, 54(1):95-104. 10.1016/0092-8674(88)90183-3, and ",".
29. Chen H.T. Xu Z. Mei C. Yu D.Y. Small S. A system of repressor gradients spatially organizes the boundaries of bicoid-dependent target genes. Cell 2012, 149(3):618-629. 10.1016/j.cell.2012.03.018, and ",".
30. Alon U. Network motifs: Theory and experimental approaches. Nat. Rev. Genet. 2007, 8(6):450-461. 10.1038/nrg2102, ",".
31. Ashe H.L. Briscoe J. The interpretation of morphogen gradients. Development 2006, 133(3):385-394. 10.1242/dev.02238, and ",".
32. Bronner G. Jackle H. Regulation and function of the terminal gap gene huckebein in the Drosophila blastoderm. The Int. J. Dev. Biol. 1996, 40(1):157-165. and ",".
33. Stathopoulos A. Levine M. Dorsal gradient networks in the Drosophila embryo. Dev. Biol. 2002, 246(1):57-67. 10.1006/dbio.2002.0652, and ",".
34. Rothe M. Wimmer E.A. Pankratz M.J. Gonzalez-Gaitan M. Jackle H. Identical transacting factor requirement for knirps and knirps-related gene expression in the anterior but not in the posterior region of the Drosophila embryo. Mech. Dev. 1994, 46(3):169-181. 10.1016/0925-4773(94)90069-8, and ",".
35. Ajuria L. Nieva C. Winkler C. Kuo D. Samper N. Andreu M.J. Helman A. Gonzalez-Crespo S. Paroush Z. Courey A.J. Jimenez G. Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila. Development 2011, 138(5):915-924. 10.1242/dev.057729, and ",".
36. Liang H.L. Nien C.Y. Liu H.Y. Metzstein M.M. Kirov N. Rushlow C. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 2008, 456(7220):400-403. 10.1038/nature07388, and ",".
37. Tsurumi A. Xia F. Li J. Larson K. LaFrance R. Li W.X. STAT is an essential activator of the zygotic genome in the early Drosophila embryo. PLOS Genet. 2011, 7(5):e1002086. 10.1371/journal.pgen.1002086, and ",".
38. Tang A.H. Neufeld T.P. Rubin G.M. Muller H.A. J. Transcriptional regulation of cytoskeletal functions and segmentation by a novel maternal pair-rule gene, lilliputian. Development 2001, 128(5):801-813. and ",".
39. Liaw G.J. Lengyel J.A. Control of tailless expression by bicoid, dorsal and synergistically interacting terminal system regulatory elements. Mech. Dev. 1993, 40(1-2):47-61. 10.1016/0925-4773(93)90087-E, and ",".
40. Nien C.Y. Liang H.L. Butcher S. Sun Y. Fu S. Gocha T. Kirov N. Manak J.R. Rushlow C. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLOS Genet. 2011, 7(10):e1002339. 10.1371/journal.pgen.1002339, and ",".
41. Papatsenko D. ClusterDraw web server: A tool to identify and visualize clusters of binding motifs for transcription factors. Bioinformatics 2007, 23(8):1032-1034. 10.1093/bioinformatics/btm047, ",".
42. Jaeger J. Modelling the Drosophila embryo. Mol. Biosyst. 2009, 5(12):1549-1568. 10.1039/b904722k, ",".
43. Longabaugh W.J. Davidson E.H. Bolouri H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 2005, 283(1):1-16. 10.1016/j.ydbio.2005.04.023, and ",".
44. Perkins T.J. Jaeger J. Reinitz J. Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. PLOS Comput. Biol. 2006, 2(5):e51. 10.1371/journal.pcbi.0020051, and ",".
45. Hader T. Wainwright D. Shandala T. Saint R. Taubert H. Bronner G. Jackle H. Receptor tyrosine kinase signaling regulates different modes of Groucho-dependent control of Dorsal. Curr. Biol. 2000, 10(1):51-54. 10.1016/S0960-9822(99)00265-1, and ",".
46. Ochoa-Espinosa A. Yucel G. Kaplan L. Pare A. Pura N. Oberstein A. Papatsenko D. Small S. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc. Natl. Acad. Sci. U.S.A 2005, 102(14):4960-4965. 10.1073/pnas.0500373102, and ",".
47. Rusch J. Levine M. Regulation of the dorsal morphogen by the Toll and torso signaling pathways: A receptor tyrosine kinase selectively masks transcriptional repression. Genes Dev. 1994, 8(11):1247-1257. 10.1101/gad.8.11.1247, and ",".
48. Courey A.J. Jia S.T. Transcriptional repression: The long and the short of it. Genes Dev. 2001, 15(21):2786-2796. 10.1101/gad.939601, and ",".
49. Cai H.N. Arnosti D.N. Levine M. Long-range repression in the Drosophila embryo. Proc. Natl. Acad. Sci. U. S. A. 1996, 93(18):9309-9314. 10.1073/pnas.93.18.9309, and ",".
50. Moran E. Jimenez G. The tailless nuclear receptor acts as a dedicated repressor in the early Drosophila embryo. Mol. Cell. Biol. 2006, 26(9):3446-3454. 10.1128/MCB.26.9.3446-3454.2006, and ",".
51. Rudolph K.M. Liaw G.J. Daniel A. Green P. Courey A.J. Hartenstein V. Lengyel J.A. Complex regulatory region mediating tailless expression in early embryonic patterning and brain development. Development 1997, 124(21):4297-4308. and ",".
52. Harrison M.M. Li X.Y. Kaplan T. Botchan M.R. Eisen M.B. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLOS Genet. 2011, 7(10):e1002266. 10.1371/journal.pgen.1002266, and ",".
53. MacArthur S. Li X.Y. Li J. Brown J.B. Chu H.C. Zeng L. Grondona B.P. Hechmer A. Simirenko L. Keranen S.V. Knowles D.W. Stapleton M. Bickel P. Biggin M.D. Eisen M.B. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009, 10(7):R80. 10.1186/gb-2009-10-7-r80, and ",".
54. Gallo S.M. Gerrard D.T. Miner D. Simich M. Des Soye B. Bergman C.M. Halfon M.S. REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 2011, 39:D118-123. 10.1093/nar/gkq999, and "," (Database issue).
55. Kulakovskiy I.V. Favorov A.V. Makeev V.J. Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinformatics 2009, 25(18):2318-2325. 10.1093/bioinformatics/btp434, and ",".
56. Papatsenko D.A. Makeev V.J. Lifanov A.P. Regnier M. Nazina A.G. Desplan C. Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers. Genome Res. 2002, 12(3):470-481. 10.1101/gr.212502, and ",".