The role of regulated mRNA stability in establishing bicoid morphogen gradient in Drosophila embryonic development

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Liu, Wei ^a   Niranjan, Mahesan ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BICOID PROTEIN; MESSENGER RNA; MORPHOGEN; UNCLASSIFIED DRUG; BICOID PROTEIN, DROSOPHILA; HOMEODOMAIN PROTEIN; TRANSACTIVATOR PROTEIN;

ARTICLE; DIFFUSION COEFFICIENT; DROSOPHILA; EGG LAYING; EMBRYO; EMBRYO DEVELOPMENT; GENE CONTROL; GENE EXPRESSION; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; POLYMERASE CHAIN REACTION; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; RNA STABILITY; STEADY STATE; STOCHASTIC MODEL; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PRENATAL DEVELOPMENT; STATISTICS; TIME; UNCERTAINTY;

ALGORITHMS; ANIMALS; DROSOPHILA MELANOGASTER; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; MODELS, GENETIC; RNA STABILITY; RNA, MESSENGER; STOCHASTIC PROCESSES; TIME FACTORS; TRANS-ACTIVATORS; UNCERTAINTY;

EID: 80052869646     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024896     Document Type: Article

References (47)

1. Turing AM, (1952) The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 237: 37-72.
2. Wolpert L, (1969) Positional information and the spatial pattern of cellular differentiation. Journal of Theoretical Biology 25: 1-47.
3. Crick F, (1970) Diffusion in embryogenesis. Nature 225: 420-422.
4. Driever W, Nüsslein-Volhard C, (1988) The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell 54: 95-104.
5. Driever W, Nüsslein-Volhard C, (1988) A gradient of bicoid protein in Drosophila embryos. Cell 54: 83-93.
6. St Johnston D, Driever W, Berleth T, Richstein S, Nüsslein-Volhard C, (1989) Multiple steps in the localization of bicoid RNA to the anterior pole of the Drosophila oocyte. Development 107: 13-19.
7. Driever W, Nüsslein-Volhard C, (1989) The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo. Nature 337: 138-143.
8. Struhl G, Struhl K, Macdonald PM, (1989) The gradient morphogen bicoid is a concentrationdependent transcriptional activator. Cell 57: 1259-1273.
9. Ephrussi A, Johnston DS, (2004) Seeing is believing: The Bicoid morphogen gradient matures. Cell 116: 143-152.
10. Houchmandzadeh B, Wieschaus E, Leibler S, (2002) Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 415: 798-802.
11. Gregor T, Bialek W, de Ruyter van Steveninck RR, Tank DW, Wieschaus EF, (2005) Diffusion and scaling during early embryonic pattern formation. Proceedings of the National Academy of Sciences USA 102: 18403-18407.
12. Gregor T, Tank DW, Wieschaus EF, Bialek W, (2007) Probing the limits to positional information. Cell 130: 153-164.
13. Gregor T, Wieschaus EF, McGregor AP, Bialek W, Tank DW, (2007) Stability and nuclear dynamics of the Bicoid morphogen gradient. Cell 130: 141-152.
14. Holloway DM, Harrison LG, Kosman D, Vanario-Alonso CE, Spirov AV, (2006) Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Developmental Dynamics 235: 2949-2960.
15. Porcher A, Dostatni N, (2010) The Bicoid morphogen system. Current Biology 20: R249-R254.
16. Löhr U, Chung HR, Beller M, Jäckle H, (2010) Bicoid- morphogen function revisited. Fly 4: 236-240.
17. Okabe-Oho Y, Murakami H, Oho S, Sasai M, (2009) Stable, precise, and reproducible patterning of Bicoid and Hunchback molecules in the early Drosophila embryo. PLoS Computational Biology 5: e1000486.
18. He F, Saunders TE, Wen Y, Cheung D, Jiao R, et al. (2010) Shaping a morphogen gradient for positional precision. Biophysical Journal 99: 697-707.
19. Grimm O, Coppey M, Wieschaus E, (2010) Modelling the Bicoid gradient. Development 137: 2253-2264.
20. Hecht I, Rappel WJ, Levine H, (2009) Determining the scale of the Bicoid morphogen gradient. Proceedings of the National Academy of Sciences USA 106: 1710-1715.
21. Wu YF, Myasnikova E, Reinitz J, (2007) Master equation simulation analysis of immunostained Bicoid morphogen gradient. BMC Systems Biology 1: 52.
22. Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81: 2340-2361.
23. Dewar MA, Kadirkamanathan V, Opper M, Sanguinetti G, (2010) Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster. BMC Systems Biology 4: 21.
24. Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY, (2007) Modeling the Bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. Developmental Biology 312: 623-630.
25. Coppey M, Boettiger AN, Berezhkovskii AM, Shvartsman SY, (2008) Nuclear trapping shapes the terminal gradient in the Drosophila embryo. Current Biology 18: 915-919.
26. Kavousanakis ME, Kanodia JS, Kim Y, Kevrekidis IG, Shvartsman SY, (2010) A compartmental model for the Bicoid gradient. Developmental Biology 345: 12-17.
27. Spirov A, Fahmy K, Schneider M, Frei E, Noll M, et al. (2009) Formation of the Bicoid morphogen gradient: an mRNA gradient dictates the protein gradient. Development 136: 605-614.
28. Cheung D, Miles C, Kreitman M, Ma J, (2011) Scaling of the Bicoid morphogen gradient by a volume-dependent production rate. Development 138: 2741-2749.
29. Bergmann S, Sandler O, Sberro H, Shnider S, Schejter E, et al. (2007) Pre-steady-state decoding of the Bicoid morphogen gradient. PLoS Biology 5: 965-991.
30. Reinitz J, Sharp DH, (1995) Mechanism of eve stripe formation. Mechanisms of Development 49: 133-158.
31. Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, et al. (2004) Dynamic control of positional information in the early Drosophila embryo. Nature 430: 368-371.
32. Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, et al. (2009) Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Computational Biology 5: e1000303.
33. Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, et al. (2009) Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology 7: e1000049.
34. Ashyraliyev M, Siggens K, Janssens H, Blom J, Akam M, et al. (2009) Gene circuit analysis of the terminal gap gene huckebein. PLoS Computational Biology 5: e1000548.
35. Fomekong-Nanfack Y, Kaandorp JA, Blom J, (2007) Efficient parameter estimation for spatiotemporal models of pattern formation: case study of Drosophila melanogaster. Bioinformatics 23: 3356-3363.
36. Surdej P, Jacobs-Lorena M, (1998) Developmental regulation of bicoid mRNA stability is mediated by the first 43 nucleotides of the 3′ untranslated region. Molecular and Cellular Biology 18: 2892-2900.
37. Poustelnikova E, Pisarev A, Blagov M, Samsonova M, Reinitz J, (2004) A database for management of gene expression data in situ. Bioinformatics 20: 2212-2221.
38. Pisarev A, Poustelnikova E, Samsonova M, Reinitz J, (2009) FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Research 37: D560-D566.
39. Cooperstock RL, Lipshitz HD, (1997) Control of mRNA stability and translation during Drosophila development. Cell and Developmental Biology 8: 541-549.
40. Salles FJ, Lieberfarb ME, Wreden C, Gergen JP, Strickland S, (1994) Coordinate initiation of Drosophila development by regulated polyadenylation of maternal messenger RNAs. Science 266: 1996-1999.
41. Little SC, Tkačik G, Kneeland TB, Wieschaus EF, Gregor T, (2011) The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biology 9: e1000596.
42. Abu-Arish A, Porcher A, Czerwonka A, Dostani N, Fradin C, (2010) High mobility of Bicoid captured by fluorescence correlation spectroscopy: implication for the rapid establishment of its gradient. Biophysical Journal 99: L33-L35.
43. Porcher A, Abu-Arish A, Huart S, Roelens B, Fradin C, et al. (2010) The time to measure positional information: maternal Hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription. Development 137: 2795-2804.
44. Kaern M, Elston TC, Blake WJ, Collins JJ, (2005) Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451464.
45. Erban R, Chapman SJ, Maini PK, (2007) A practical guide to stochastic simulations of reactiondiffusion processes. Arxiv preprint arXiv: 07041908.
46. Dilão R, Muraro D, (2010) mRNA diffusion explains protein gradients in Drosophila early development. Journal of Theoretical Biology 264: 847-853.
47. Foe VE, Alberts BM, (1983) Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis. Journal of Cell Science 61: 31-70.