The evolution of ultraconserved elements with different phylogenetic origins

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Ryu, Taewoo ^a,b   Seridi, Loqmane ^a,b   Ravasi, Timothy ^a,b  

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

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Developmental enhancers; Genome evolution; Marine biology; Transcriptional regulatory networks; Ultraconserved elements

Indexed keywords

APOPTOSIS; COMMUNITY COMPOSITION; DNA; EVOLUTIONARY BIOLOGY; GENE; GENOME; PHYLOGENETICS; SPECIES DIVERSITY;

ANIMALIA; EUKARYOTA; INVERTEBRATA; METAZOA; VERTEBRATA;

DNA; TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; BINDING SITE; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; DNA; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

MLCS; MLOWN;

EID: 84870382048     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-236     Document Type: Article

References (65)

1. Ultraconserved elements in the human genome. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D, Science (New York, NY) 2004 304 5675 1321 1325 10.1126/science.1098119
2. Widespread ultraconservation divergence in primates. Ovcharenko I, Mol Biol Evol 2008 25 8 1668 1676 10.1093/molbev/msn116 18492662
3. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS, Genome Res 2005 15 6 800 808 10.1101/gr.3545105 15899965
4. Ultraconserved elements between the genomes of the plants Arabidopsis thaliana and rice. Zheng W-X, Zhang C-T, J Biomol Struct Dyn 2008 26 1 8 10.1080/07391102.2008.10507218 18533721
5. Conservation patterns in different functional sequence categories of divergent Drosophila species. Papatsenko D, Kislyuk A, Levine M, Dubchak I, Genomics 2006 88 4 431 442 10.1016/j.ygeno.2006.03.012 16697139
6. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M, Genes Dev 2007 21 6 708 718 10.1101/gad.1525507 17369403
7. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE, Nature 2007 446 7138 926 929 10.1038/nature05676 17361132
8. In vivo enhancer analysis of human conserved non-coding sequences. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, et al. Nature 2006 444 7118 499 502 10.1038/nature05295 17086198
9. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA, Nat Genet 2008 40 2 158 160 10.1038/ng.2007.55 18176564
10. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Derti A, Roth FP, Church GM, Wu C, Nat Genet 2006 38 1216 1220 10.1038/ng1888 16998490
11. SNPs in ultraconserved elements and familial breast cancer risk. Yang R, Frank B, Hemminki K, Bartram CR, Wappenschmidt B, Sutter C, Kiechle M, Bugert P, Schmutzler RK, Arnold N, et al. Carcinogenesis 2008 29 2 351 355 18174240
12. An SNP in an ultraconserved regulatory element affects Dlx5/Dlx6 regulation in the forebrain. Poitras L, Yu M, Lesage-Pelletier C, Macdonald RB, Gagn J-P, Hatch G, Kelly I, Hamilton SP, Rubenstein JLR, Poirier GG, et al. Development (Cambridge, England) 2010 137 18 3089 3097 10.1242/dev.051052
13. Deletion of ultraconserved elements yields viable mice. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM, PLoS biology 2007 5 9 234 e234 10.1371/journal.pbio.0050234 17803355
14. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D, Nature 2006 441 7089 87 90 10.1038/nature04696 16625209
15. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Stephen S, Pheasant M, Makunin IV, Mattick JS, Mol Biol Evol 2008 25 2 402 408 10.1093/molbev/msm268 18056681
16. Human genome ultraconserved elements are ultraselected. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D, Science (New York, NY) 2007 317 5840 915 915 10.1126/science.1142430
17. Ultraconserved coding regions outside the homeobox of mammalian Hox genes. Lin Z, Ma H, Nei M, BMC Evol Biol 2008 8 260 260 10.1186/1471-2148-8-260 18816392
18. Identification and characterization of new long conserved noncoding sequences in vertebrates. Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi KR, Toyoda A, Fukumura R, Murata T, Sakaki Y, et al. Mammalian genome: official journal of the International Mammalian Genome Society 2008 19 10-12 703 712
19. TimeTree: a public knowledge-base of divergence times among organisms. Hedges SB, Dudley J, Kumar S, Bioinformatics (Oxford, England) 2006 22 23 2971 2972 10.1093/bioinformatics/btl505
20. Versatile and open software for comparing large genomes. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL, Genome Biol 2004 5 2 12 R12 10.1186/gb-2004-5-2-r12 14759262
21. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead B, Trapnell C, Pop M, Salzberg SL, Genome Biol 2009 10 3 25 R25 10.1186/gb-2009-10-3-r25 19261174
22. UCSC Genome Browser, http://genome.ucsc.edu/
23. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Kohany O, Gentles AJ, Hankus L, Jurka J, BMC Bioinforma 2006 7 474 474 10.1186/1471-2105-7-474
24. Tandem repeats finder: a program to analyze DNA sequences. Benson G, Nucleic Acids Res 1999 27 2 573 580 10.1093/nar/27.2.573 9862982
25. ltraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC, Syst Biol 2012
26. Positive and negative selection in murine ultra-conserved noncoding elements. Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, Keightley PD, Mol Biol Evol 2011 28 9 2651 2660 10.1093/molbev/msr093 21478460
27. Population bottlenecks as a potential major shaping force of human genome architecture. Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N, PLoS genetics 2007 3 7 119 10.1371/journal.pgen.0030119 17658953
28. Large number of ultraconserved elements were already present in the jawed vertebrate ancestor. Wang J, Lee AP, Kodzius R, Brenner S, Venkatesh B, Mol Biol Evol 2009 26 3 487 490 19052148
29. Adaptive evolution of conserved noncoding elements in mammals. Kim SY, Pritchard JK, PLoS genetics 2007 3 9 1572 1586 17845075
30. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M, Bioinformatics 2010 26 18 531 i539 10.1093/bioinformatics/btq376 20823318
31. Ion homeostasis, channels, and transporters: an update on cellular mechanisms. Dubyak GR, Adv Physiol Educ 2004 28 1-4 143 154 15545343
32. Control of developmental regulators by Polycomb in human embryonic stem cells. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K-i, et al. Cell 2006 125 2 301 313 10.1016/j.cell.2006.02.043 16630818
33. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. Cell 2006 125 2 315 326 10.1016/j.cell.2006.02.041 16630819
34. Functional protein-protein interaction of drug metabolizing enzymes. Ishii Y, Takeda S, Yamada H, Oguri K, Front Biosci 2005 10 887 895 10.2741/1583 15569627
35. Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Chiang CWK, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu C-T, Genetics 2008 180 2277 2293 10.1534/genetics.108.096537 18957701
36. An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Lampe X, Samad OA, Guiguen A, Matis C, Remacle S, Picard JJ, Rijli FM, Rezsohazy R, Nucleic Acids Res 2008 36 10 3214 3225 10.1093/nar/gkn148 18417536
37. Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts. Rödelsperger C, Köhler S, Schulz MH, Manke T, Bauer S, Robinson PN, Genomics 2009 94 308 316 10.1016/j.ygeno.2009.07.005 19660540
38. Horizontal gene transfer, genome innovation and evolution. Gogarten JP, Townsend JP, Nat Rev Microbiol 2005 3 9 679 687 10.1038/nrmicro1204 16138096
39. Dispensability of mammalian DNA. McLean C, Bejerano G, Genome Res 2008 18 11 1743 1751 10.1101/gr.080184.108 18832441
40. Initial sequencing and analysis of the human genome. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Nature 2001 409 6822 860 921 10.1038/35057062 11237011
41. Are «ultraconserved» genetic elements really indispensable? Gross L, PLoS biology 2007 5 9 253 e253 10.1371/journal.pbio.0050253 20076686
42. The Amphimedon queenslandica genome and the evolution of animal complexity. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, et al. Nature 2010 466 7307 720 726 10.1038/nature09201 20686567
43. The dynamic genome of Hydra. Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, et al. Nature 2010 464 7288 592 596 10.1038/nature08830 20228792
44. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, et al. Science 2007 317 5834 86 94 10.1126/science.1139158 17615350
45. The genome of the sea urchin Strongylocentrotus purpuratus. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, et al. Science (New York, NY) 2006 314 5801 941 952
46. Algorithm of OMA for large-scale orthology inference. Roth AC, Gonnet GH, Dessimoz C, BMC Bioinforma 2008 9 518 10.1186/1471-2105-9-518
47. Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits. Dessimoz C, Boeckmann B, Roth AC, Gonnet GH, Nucleic Acids Res 2006 34 11 3309 3316 10.1093/nar/gkl433 16835308
48. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL, Nucleic Acids Res 2010 38 196 203
49. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Edgar RC, BMC Bioinforma 2004 5 113 113 10.1186/1471-2105-5-113
50. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 10 2731 2739 10.1093/molbev/msr121 21546353
51. Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network. Ryu T, Mavromatis CH, Bayer T, Voolstra CR, Ravasi T, BMC Syst Biol 2011 5 58 58 10.1186/1752-0509-5-58 21526989
52. Broad phylogenomic sampling improves resolution of the animal tree of life. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, et al. Nature 2008 452 7188 745 749 10.1038/nature06614 18322464
53. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410 2231712
54. An efficient algorithm for large-scale detection of protein families. Enright AJ, Van Dongen S, Ouzounis CA, Nucleic Acids Res 2002 30 7 1575 1584 10.1093/nar/30.7.1575 11917018
55. Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. Cannistraci CV, Lobato GA, Ravasi T, submitted
56. NCBI Reference Sequences: current status, policy and new initiatives. Pruitt KD, Tatusova T, Klimke W, Maglott DR, Nucleic Acids Res 2009 37 32 36 10.1093/nar/gkn721
57. InterProScan-an integration platform for the signature-recognition methods in InterPro. Zdobnov EM, Apweiler R, Bioinformatics 2001 17 9 847 848 10.1093/bioinformatics/17.9.847 11590104
58. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Huang DW, Sherman BT, Lempicki RA, Nat Protoc 2009 4 1 44 57 19131956
59. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Charif D, Lobry JR, Structural Approaches to Sequence Evolution 2007 1 207 232
60. STAMP: a web tool for exploring DNA-binding motif similarities. Mahony S, Benos PV, Nucleic Acids Res 2007 35 253 258
61. The rapid generation of mutation data matrices from protein sequences. Jones DT, Taylor WR, Thornton JM, Comput Appl Biosci 1992 8 3 275 282 1633570
62. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 4 406 425 3447015
63. Oosting J, Eilers P, Menezes R, Quantsmooth: Quantile smoothing and genomic visualization of array data 2009
64. NCBI Gene, http://www.ncbi.nlm.nih.gov/gene/
65. GeneCards Version 3: the human gene integrator. Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, et al. Database (Oxford) 2010 020