The precise timeline of transcriptional regulation reveals causation in mouse somitogenesis network

BMC Developmental Biology

Volumn 13, Issue 1, 2013, Pages

  Fongang, Bernard ^a   Kudlicki, Andrzej ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Maximum Entropy deconvolution; Somitogenesis; Transcriptional regulation

Indexed keywords

VERTEBRATA;

FIBROBLAST GROWTH FACTOR; NOTCH RECEPTOR; WNT PROTEIN;

ALGORITHM; ANIMAL; ANIMAL EMBRYO; ARTICLE; EMBRYO DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOUSE; PHYSIOLOGY; SIGNAL TRANSDUCTION; SOMITE; TIME;

ALGORITHMS; ANIMALS; EMBRYO, MAMMALIAN; EMBRYONIC DEVELOPMENT; FIBROBLAST GROWTH FACTORS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; MICE; RECEPTORS, NOTCH; SIGNAL TRANSDUCTION; SOMITES; TIME FACTORS; TRANSCRIPTION, GENETIC; WNT PROTEINS;

EID: 84889057157     PISSN: None     EISSN: 1471213X     Source Type: Journal    
DOI: 10.1186/1471-213X-13-42     Document Type: Article

References (61)

1. From head to tail: links between the segmentation clock and antero-posterior patterning of the embryo. Dubrulle J, Pourquie O, Curr Opin Genet Dev 2002 12 519 523 10.1016/S0959-437X(02)00335-0 12200156
2. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Dequeant ML, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, Pourquie O, Science 2006 314 1595 1598 10.1126/science.1133141 17095659
3. Dynamic expression of lunatic fringe suggests a link between notch signaling and an autonomous cellular oscillator driving somite segmentation. Aulehla A, Johnson RL, Dev Biol 1999 207 49 61 10.1006/dbio.1998.9164 10049564
4. Function of the retinoic acid receptors (Rars) during development.1. craniofacial and skeletal abnormalities in Rar double mutants. Lohnes D, Mark M, Mendelsohn C, Dolle P, Dierich A, Gorry P, Gansmuller A, Chambon P, Development 1994 120 2723 2748 7607067
5. Hemivertebra: prenatal diagnosis, incidence and characteristics. Goldstein I, Makhoul IR, Weissman A, Drugan A, Fetal Diagn Ther 2005 20 121 126 10.1159/000082435 15692206
6. Segmentation in vertebrates: clock and gradient finally joined. Aulehla A, Herrmann BG, Genes Dev 2004 18 2060 2067 10.1101/gad.1217404 15342488
7. Wnt3A plays a major role in the segmentation clock controlling somitogenesis. Aulehla A, Wehrle C, Brand-Saberi B, Kemler R, Gossler A, Kanzler B, Herrmann BG, Dev Cell 2003 4 395 406 10.1016/S1534-5807(03)00055-8 12636920
8. Glycosyltransferase activity of fringe modulates notch-delta interactions. Bruckner K, Perez L, Clausen H, Cohen S, Nature 2000 406 411 415 10.1038/35019075 10935637
9. Clock and wavefront model for control of number of repeated structures during animal morphogenesis. Cooke J, Zeeman EC, J Theor Biol 1976 58 455 476 10.1016/S0022-5193(76)80131-2 940335
10. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Palmeirim I, Henrique D, IshHorowicz D, Pourquie O, Cell 1997 91 639 648 10.1016/S0092-8674(00)80451-1 9393857
11. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Lewis J, Curr Biol 2003 13 1398 1408 10.1016/S0960-9822(03)00534-7 12932323
12. A phase-ordered microarray screen for cyclic genes in zebrafish reveals her genes as the conserved core of the somitogenesis clock. Roellig D, Kumichel A, Krol A, Dequeant ML, Tassy O, Hattem G, Glynn E, Oates A, Pourquie O, Mech Dev 2009 126 252 S253
13. Evolutionary plasticity of segmentation clock networks. Krol AJ, Roellig D, Dequeant ML, Tassy O, Glynn E, Hattem G, Mushegian A, Oates AC, Pourquie O, Development 2011 138 2783 2792 10.1242/dev.063834 21652651
14. Notch is a critical component of the mouse somitogenesis oscillator and is essential for the formation of the somites. Ferjentsik Z, Hayashi S, Dale JK, Bessho Y, Herreman A, De Strooper B, del Monte G, de la Pompa JL, Maroto M, PLoS Genet 2009 5 1000662 10.1371/journal.pgen.1000662 19779553
15. The segmentation clock mechanism moves up a notch. Gibb S, Maroto M, Dale JK, Trends Cell Biol 2010 20 593 600 10.1016/j.tcb.2010.07.001 20724159
16. A Notch feeling of somite segmentation and beyond. Rida PCG, Le Minh N, Jiang YJ, Dev Biol 2004 265 2 22 10.1016/j.ydbio.2003.07.003 14697349
17. The segmentation clock: converting embryonic time into spatial pattern. Pourquie O, Science 2003 301 328 330 10.1126/science.1085887 12869750
18. Vertebrate somitogenesis: a novel paradigm for animal segmentation? Pourquie O, Int J Dev Biol 2003 47 597 603 14756335
19. Oscillating signaling pathways during embryonic development. Aulehla A, Pourquie O, Curr Opin Cell Biol 2008 20 632 637 10.1016/j.ceb.2008.09.002 18845254
20. From dynamic expression patterns to boundary formation in the presomitic mesoderm. Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, de Angelis MH, PLoS Comput Biol 2012 8 1002586 10.1371/journal.pcbi.1002586 22761566
21. A multi-cell, multi-scale model of vertebrate segmentation and somite formation. Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA, PLoS Comput Biol 2011 7 1002155 10.1371/journal.pcbi.1002155 21998560
22. Segmental patterning of the vertebrate embryonic axis. Dequeant ML, Pourquie O, Nat Rev Genet 2008 9 370 382 18414404
23. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Tu BP, Kudlicki A, Rowicka M, McKnight SL, Science 2005 310 1152 1158 10.1126/science.1120499 16254148
24. High-resolution timing of cell cycle-regulated gene expression. Rowicka M, Kudlicki A, Tu BP, Otwinowski Z, Proc Natl Acad Sci U S A 2007 104 16892 16897 10.1073/pnas.0706022104 17827275
25. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B, Mol Biol Cell 1998 9 3273 3297 10.1091/mbc.9.12.3273 9843569
26. Analyzing time series gene expression data. Bar-Joseph Z, Bioinformatics 2004 20 2493 2503 10.1093/bioinformatics/bth283 15130923
27. Efficient method for finding minimum of function of several-variables without calculating derivatives. Powell MJD, Comput J 1964 7 155 10.1093/comjnl/7.2.155
28. Comparison of pattern detection methods in microarray time series of the segmentation clock. Dequeant ML, Ahnert S, Edelsbrunner H, Fink TMA, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, et al. PLoS One 2008 3 2856 10.1371/journal.pone.0002856 18682743
29. A nomenclature for prospective somites and phases of cyclic gene expression in the presomitic mesoderm. Pourquie O, Tam PPL, Dev Cell 2001 1 619 620 10.1016/S1534-5807(01)00082-X 11709182
30. FGF signaling acts upstream of the NOTCH and WNT signaling pathways to control segmentation clock oscillations in mouse somitogenesis. Wahl MB, Deng C, Lewandoski M, Pourquie O, Development 2007 134 4033 4041 10.1242/dev.009167 17965051
31. On periodicity and directionality of somitogenesis. Aulehla A, Pourquie O, Anat Embryol 2006 211 3 S8
32. Periodic notch inhibition by Lunatic Fringe underlies the chick segmentation clock. Maroto M, Dale K, Pourquie O, Faseb J 2003 17 814 A814
33. Synchronised cycling gene oscillations in presomitic mesoderm cells require cell-cell contact. Maroto M, Dale JK, Dequeant ML, Petit AC, Pourquie O, Int J Dev Biol 2005 49 309 315 10.1387/ijdb.041958mm 15906246
34. Wnt3a/beta-catenin signaling controls posterior body development by coordinating mesoderm formation and segmentation. Dunty WC, Biris KK, Chalamalasetty RB, Taketo MM, Lewandoski M, Yamaguchi TP, Development 2008 135 85 94 18045842
35. beta-Catenin hits chromatin: regulation of Wnt target gene activation. Mosimann C, Hausmann G, Basler K, Nat Rev Mol Cell Biol 2009 10 276 19305417
36. Transcription under the control of nuclear Arm/beta-catenin. Stadeli R, Hoffmans R, Basler K, Curr Biol 2006 16 378 R385 10.1016/j.cub.2006.04.019 16713950
37. A beta-catenin gradient links the clock and wavefront systems in mouse embryo segmentation. Aulehla A, Wiegraebe W, Baubet V, Wahl MB, Deng CX, Taketo M, Lewandoski M, Pourquie O, Nat Cell Biol 2008 10 186 10.1038/ncb1679 18157121
38. Signaling gradients during paraxial mesoderm development. Aulehla A, Pourquie O, Cold Spring Harb Perspect Biol 2010 2 000869 20182616
39. Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules. Yu SR, Burkhardt M, Nowak M, Ries J, Petrasek Z, Scholpp S, Schwille P, Brand M, Nature 2009 461 533 10.1038/nature08391 19741606
40. The mouse Fgf8 gene encodes a family of polypeptides and is expressed in regions that direct outgrowth and patterning in the developing embryo. Crossley PH, Martin GR, Development 1995 121 439 451 7768185
41. Fgf-8 expression in the post-gastrulation mouse suggests roles in the development of the face, limbs and central-nervous-system. Heikinheimo M, Lawshe A, Shackleford GM, Wilson DB, Macarthur CA, Mech Dev 1994 48 129 138 10.1016/0925-4773(94)90022-1 7873403
42. Distinct functions of the major Fgf8 spliceform, Fgf8b, before and during mouse gastrulation. Guo QX, Li JYH, Development 2007 134 2251 2260 10.1242/dev.004929 17507393
43. O Pourquie: fgf8 mRNA decay establishes a gradient that couples axial elongation to patterning in the vertebrate embryo. Dubrulle J, Nature 2004 427 419 422 10.1038/nature02216 14749824
44. Notch1 is required for the coordinate segmentation of somites. Conlon RA, Reaume AG, Rossant J, Development 1995 121 1533 1545 7789282
45. Periodic Lunatic fringe expression is controlled during segmentation by a cyclic transcriptional enhancer responsive to notch signaling. Morales AV, Yasuda Y, Ish-Horowicz D, Dev Cell 2002 3 63 74 10.1016/S1534-5807(02)00211-3 12110168
46. Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis. Cole SE, Levorse JM, Tilghman SM, Vogt TF, Dev Cell 2002 3 75 84 10.1016/S1534-5807(02)00212-5 12110169
47. Dynamic expression and essential functions of Hes7 in somite segmentation. Bessho Y, Sakata R, Komatsu S, Shiota K, Yamada S, Kageyama R, Genes Dev 2001 15 2642 2647 10.1101/gad.930601 11641270
48. Periodic repression by the bHLH factor Hes7 is an essential mechanism for the somite segmentation clock. Bessho Y, Hirata H, Masamizu Y, Kageyama R, Genes Dev 2003 17 1451 1456 10.1101/gad.1092303 12783854
49. The initiation and propagation of hes7 oscillation are cooperatively regulated by fgf and notch signaling in the somite segmentation clock. Niwa Y, Masamizu Y, Liu T, Nakayama R, Deng CX, Kageyama R, Dev Cell 2007 13 298 304 10.1016/j.devcel.2007.07.013 17681139
50. Coupling segmentation to axis formation. Dubrulle J, Pourquie O, Development 2004 131 5783 5793 10.1242/dev.01519 15539483
51. A segmentation clock with two-segment periodicity in insects. Sarrazin AF, Peel AD, Averof M, Science 2012 336 338 341 10.1126/science.1218256 22403177
52. Embryonic lethality caused by apoptosis during gastrulation in mice lacking the gene of the ADP-ribosylation factor-related protein 1. Mueller AG, Moser M, Kluge R, Leder S, Blum M, Buttner R, Joost HG, Schurmann A, Mol Cell Biol 2002 22 1488 1494 10.1128/MCB.22.5.1488-1494.2002 11839814
53. Least-squares frequency-analysis of unequally spaced data. Lomb NR, Astrophy Space Sci 1976 39 447 462 10.1007/BF00648343
54. Tests of significance in harmonic analysis. Fisher, Proc Roy Soc Ser A 1929 125 54 59 10.1098/rspa.1929.0151
55. Sivia DS, Skilling J, Data analysis: a Bayesian tutorial Oxford, New York: Oxford University Press 2 2006
56. Deconvolution of astronomical images using the multiscale maximum entropy method. Pantin E, Starck JL, Astronomy Astrophy Suppl Ser 1996 118 575 585 10.1051/aas:1996221
57. Hypomorphic expression of Dkk1 in the doubleridge mouse: dose dependence and compensatory interactions with Lrp6. MacDonald BT, Adamska M, Meisler MH, Development 2004 131 2543 2552 10.1242/dev.01126 15115753
58. Transcriptional oscillation of Lunatic fringe is essential for somitogenesis. Serth K, Schuster-Gossler K, Cordes R, Gossler A, Genes Dev 2003 17 912 925 10.1101/gad.250603 12670869
59. Noise-resistant and synchronized oscillation of the segmentation clock. Horikawa K, Ishimatsu K, Yoshimoto E, Kondo S, Takeda H, Nature 2006 441 719 723 10.1038/nature04861 16760970
60. Emergence of traveling waves in the zebrafish segmentation clock. Ishimatsu K, Takamatsu A, Takeda H, Development 2010 137 1595 1599 10.1242/dev.046888 20392739
61. SCEPTRANS: an online tool for analyzing periodic transcription in yeast. Kudlicki A, Rowicka M, Otwinowski Z, Bioinformatics 2007 23 1559 1561 10.1093/bioinformatics/btm126 17400726