Time-based patterning in development: The role of oscillating gene expression

Transcription

Volumn 2, Issue 3, 2011, Pages 124-129

  Moreno Risueno, Miguel A ^a   Benfey, Philip N ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Biological clock; Development; Gene expression; Oscillation; Patterning; Time

Indexed keywords

BETA CATENIN; DEATH RECEPTOR 5; NOTCH RECEPTOR; TRANSCRIPTION FACTOR; WNT PROTEIN;

ARTICLE; BINDING SITE; BIOLOGICAL RHYTHM; CONVERGENT EVOLUTION; DEVELOPMENTAL GENETICS; DEVELOPMENTAL STAGE; DR5 GENE; EMBRYO DEVELOPMENT; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; MARKER GENE; MUSCULOSKELETAL DEVELOPMENT; NONHUMAN; PLANT DEVELOPMENT; PROCESS DEVELOPMENT; SIGNAL TRANSDUCTION;

ANIMALIA; VERTEBRATA;

EID: 79958764876     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.2.3.15637     Document Type: Article

References (33)

1. Dong G, Kim YI, Golden SS. Simplicity and complexity in the cyanobacterial circadian clock mechanism. Curr Opin Genet Dev 2010; 20:619-625.
2. Jolma IW, Laerum OD, Lillo C, Ruoff P. Circadian oscillators in eukaryotes. Wiley Interdiscip Rev Syst Biol Med 2010; 2:533-549.
3. Doherty CJ, Kay SA. Circadian control of global gene expression patterns. Annu Rev Genet 2010; 44:419-444.
4. Harmer SL. The circadian system in higher plants. Annu Rev Plant Biol 2009; 60:357-377.
5. de Montaigu A, Toth R, Coupland G. Plant development goes like clockwork. Trends Genet 2010; 26:296-306.
6. Khapre RV, Samsa WE, Kondratov RV. Circadian regulation of cell cycle: Molecular connections between aging and the circadian clock. Ann Med 2010; 42:404-415.
7. Aulehla A, Pourquie O. Oscillating signaling pathways during embryonic development. Curr Opin Cell Biol 2008; 20:632-637
8. Kageyama R, Niwa Y, Shimojo H. Rhythmic gene expression in somite formation and neural development. Mol Cells 2009; 27:497-502.
9. Kageyama R, Niwa Y, Shimojo H, Kobayashi T, Ohtsuka T. Ultradian oscillations in Notch signaling regulate dynamic biological events. Curr Top Dev Biol 2010; 92:311-331.
10. Lewis J, Hanisch A, Holder M. Notch signaling, the segmentation clock and the patterning of vertebrate somites. J Biol 2009; 8:44.
11. Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science 2010; 329:1306-1311.
12. Lewis J. From signals to patterns: space, time and mathematics in developmental biology. Science 2008; 322:399-403.
13. Dequeant ML, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, et al. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 2006; 314:1595-1598.
14. Pourquie O. The segmentation clock: converting embryonic time into spatial pattern. Science 2003; 301:328-330.
15. De Smet I, Tetsumura T, De Rybel B, Frey NF, Laplaze L, Casimiro I, et al. Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis. Development 2007; 134:681-690.
16. Nakamura A, Higuchi K, Goda H, Fujiwara MT, Sawa S, Koshiba T, et al. Brassinolide induces IAA5, IAA19 and DR5, a synthetic auxin response element in Arabidopsis, implying a cross talk point of brassi-nosteroid and auxin signaling. Plant Physiol 2003; 133:1843-1853.
17. Heisler MG, Ohno C, Das P, Sieber P, Reddy GV, Long JA, et al. Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Curr Biol 2005; 15:1899-1911.
18. Petersson SV, Johansson AI, Kowalczyk M, Makoveychuk A, Wang JY, Moritz T, et al. An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 2009; 21:1659-1668.
19. Dequeant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, et al. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One 2008; 3:2856.
20. Jiang YJ, Aerne BL, Smithers L, Haddon C, Ish-Horowicz D, Lewis J. Notch signalling and the synchronization of the somite segmentation clock. Nature 2000; 408:475-479.
21. Schroter C, Herrgen L, Cardona A, Brouhard GJ, Feldman B, Oates AC. Dynamics of zebrafish somi-togenesis. Dev Dyn 2008; 237:545-553.
22. Benkova E, Michniewicz M, Sauer M, Teichmann T, Seifertova D, Jurgens G, et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 2003; 115:591-602.
23. Moller B, Weijers D. Auxin control of embryo patterning. Cold Spring Harb Perspect Biol 2009; 1:1545.
24. Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, et al. Spatio temp oral regulation of cell cycle genes by SHORTROOT links patterning and growth. Nature 2010; 466:128-132.
25. Nakajima K, Sena G, Nawy T, Benfey PN. Intercellular movement of the putative transcription factor SHR in root patterning. Nature 2001; 413:307-311.
26. Helariutta Y, Fukaki H, Wysocka-Diller J, Nakajima K, Jung J, Sena G, et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 2000; 101:555-567
27. Carlsbecker A, Lee JY, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, et al. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 2010; 465:316-321.
28. Gomez C, Ozbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquie O. Control of segment number in vertebrate embryos. Nature 2008; 454:335-339.
29. Heisler MG, Hamant O, Krupinski P, Uyttewaal M, Ohno C, Jonsson H, et al. Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport. PLoS Biol 2010; 8:1000516.
30. Novak B, Tyson JJ. Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 2008; 9:981-991.
31. Hubbard KE, Robertson FC, Dalchau N, Webb AA. Systems analyses of circadian networks. Mol Biosyst 2009; 5:1502-1511.
32. Hirata H, Bessho Y, Kokubu H, Masamizu Y, Yamada S, Lewis J, et al. Instability of Hes7 protein is crucial for the somite segmentation clock. Nat Genet 2004; 36:750-754.
33. Goldbeter A, Pourquie O. Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol 2008; 252:574-85.