Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Ryu, Taewoo ^a   Mavromatis, Charalampos H ^a   Bayer, Till ^a   Voolstra, Christian R ^a   Ravasi, Timothy ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

ACROPORA MILLEPORA; ANTHOZOA; EUMETAZOA;

TRANSCRIPTION FACTOR;

ANIMAL; ANTHOZOA; ARTICLE; BIOLOGICAL MODEL; DNA FOOTPRINTING; DNA SEQUENCE; EVOLUTION; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; PHYLOGENY; SEA; SPECIES DIFFERENCE;

ANIMALS; ANTHOZOA; BIOLOGICAL EVOLUTION; DNA FOOTPRINTING; GENE EXPRESSION PROFILING; GENOMICS; MODELS, BIOLOGICAL; OCEANS AND SEAS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

EID: 79955165689     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-58     Document Type: Article

References (45)

1. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010, 140(5):744-752. 10.1016/j.cell.2010.01.044, 2836267, 20211142.
2. Hinman VF, Davidson EH. Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci USA 2007, 104(49):19404-19409. 10.1073/pnas.0709994104, 2148302, 18042699.
3. Oliveri P, Tu Q, Davidson EH. Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci USA 2008, 105(16):5955-5962. 10.1073/pnas.0711220105, 2329687, 18413610.
4. van Oppen MJ, Gates RD. Conservation genetics and the resilience of reef-building corals. Mol Ecol 2006, 15(13):3863-3883. 10.1111/j.1365-294X.2006.03026.x, 17054489.
5. Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias-Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME. Coral reefs under rapid climate change and ocean acidification. Science 2007, 318(5857):1737-1742. 10.1126/science.1152509, 18079392.
6. Hughes TP, Rodrigues MJ, Bellwood DR, Ceccarelli D, Hoegh-Guldberg O, McCook L, Moltschaniwskyj N, Pratchett MS, Steneck RS, Willis B. Phase shifts, herbivory, and the resilience of coral reefs to climate change. Curr Biol 2007, 17(4):360-365. 10.1016/j.cub.2006.12.049, 17291763.
7. DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. Mol Ecol 2008, 17(17):3952-3971. 10.1111/j.1365-294X.2008.03879.x, 18662230.
8. Voolstra CR, Schwarz JA, Schnetzer J, Sunagawa S, Desalvo MK, Szmant AM, Coffroth MA, Medina M. The host transcriptome remains unaltered during the establishment of coral-algal symbioses. Mol Ecol 2009, 18(9):1823-1833. 10.1111/j.1365-294X.2009.04167.x, 19317843.
9. DeSalvo MK, Sunagawa S, Voolstra CR, Medina M. Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmata. Marine Ecology Progress Series 2010, 402:97-113.
10. Portune KJ, Voolstra CR, Medina M, Szmant AM. Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata. Marine Genomics 2010, 3(1):51-62.
11. Voolstra CR, Schnetzer J, Peshkin L, Randall CJ, Szmant AM, Medina M. Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. BMC Genomics 2009, 10:627. 10.1186/1471-2164-10-627, 2807443, 20030803.
12. Polato NR, Voolstra CR, Schnetzer J, DeSalvo MK, Randall CJ, Szmant AM, Medina M, Baums IB. Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata. PLoS One 2010, 5(6):e11221. 10.1371/journal.pone.0011221, 2890407, 20585643.
13. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
14. Schwarz JA, Brokstein PB, Voolstra C, Terry AY, Manohar CF, Miller DJ, Szmant AM, Coffroth MA, Medina M. Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics 2008, 9:97. 10.1186/1471-2164-9-97, 2291459, 18298846.
15. Miller DJ, Hemmrich G, Ball EE, Hayward DC, Khalturin K, Funayama N, Agata K, Bosch TCG. The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss. Genome Biol 2007, 8(4):R59. 10.1186/gb-2007-8-4-r59, 1896004, 17437634.
16. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA. DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 2008, (36 Database):D88-92.
17. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res 2000, 28(1):289-291. 10.1093/nar/28.1.289, 102387, 10592249.
18. Shin CJ, Davis MJ, Ragan MA. Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics 2009, 9(23):5256-5266. 10.1002/pmic.200900262, 19834899.
19. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
21. Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17(9):847-848. 10.1093/bioinformatics/17.9.847, 11590104.
22. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res 2010, (38 Database):D211-222.
23. Baker ME. Origin and diversification of steroids: co-evolution of enzymes and nuclear receptors. Mol Cell Endocrinol 2011, 334(1-2):14-20. 10.1016/j.mce.2010.07.013, 20654689.
24. Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner J. The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci 2005, 62(4):435-445. 10.1007/s00018-004-4416-1, 15719170.
25. McDonald J. Handbook of Biological Statistics. 2009, Baltimore, Maryland.: Sparky House Publishing, 2.
26. Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res 2006, 16(3):428-435. 10.1101/gr.4526006, 1415213, 16510899.
27. Brown KR, Jurisica I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 2007, 8(5):R95. 10.1186/gb-2007-8-5-r95, 1929159, 17535438.
28. Wuchty S, Barabasi AL, Ferdig MT. Stable evolutionary signal in a yeast protein interaction network. BMC Evol Biol 2006, 6:8. 10.1186/1471-2148-6-8, 1395346, 16441898.
29. O'Brien KP, Remm M, Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, (33 Database):D476-480.
30. Hulsen T, Huynen MA, de Vlieg J, Groenen PM. Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006, 7(4):R31. 10.1186/gb-2006-7-4-r31, 1557999, 16613613.
31. Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 2010, (38 Database):D196-203.
32. Ochman H, Liu R, Rocha EP. Erosion of interaction networks in reduced and degraded genomes. J Exp Zool B Mol Dev Evol 2007, 308(1):97-103.
33. Guan Y, Dunham MJ, Troyanskaya OG. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 2007, 175(2):933-943. 10.1534/genetics.106.064329, 1800624, 17151249.
34. Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ?. Trends Genet 2009, 25(5):210-216. 10.1016/j.tig.2009.03.004, 19368988.
35. Deschamps J, van Nes J. Developmental regulation of the Hox genes during axial morphogenesis in the mouse. Development 2005, 132(13):2931-2942. 10.1242/dev.01897, 15944185.
36. Wang S, Zhang L, Meyer E, Matz MV. Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora. Genome Biol 2009, 10(11):R126. 10.1186/gb-2009-10-11-r126, 3091320, 19900279.
37. Kamm K, Schierwater B, Jakob W, Dellaporta SL, Miller DJ. Axial patterning and diversification in the cnidaria predate the Hox system. Curr Biol 2006, 16(9):920-926. 10.1016/j.cub.2006.03.036, 16563766.
38. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 2007, 317(5834):86-94. 10.1126/science.1139158, 17615350.
39. Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 2004, 431(7004):67-71. 10.1038/nature02709, 15343333.
40. Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis. PLoS One 2007, 2(1):e153. 10.1371/journal.pone.0000153, 1779807, 17252055.
41. Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC. More than just orphans: are taxonomically-restricted genes important in evolution?. Trends Genet 2009, 25(9):404-413. 10.1016/j.tig.2009.07.006, 19716618.
42. Pinney JW, Amoutzias GD, Rattray M, Robertson DL. Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci USA 2007, 104(51):20449-20453. 10.1073/pnas.0706339104, 2154451, 18077348.
43. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009, 10(4):252-263. 10.1038/nrg2538, 19274049.
44. Aiyar A. The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment. Methods Mol Biol 2000, 132:221-241.
45. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008, 9(4):299-306. 10.1093/bib/bbn017, 2562624, 18417537.