Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders

Genome Biology and Evolution

Volumn 5, Issue 12, 2013, Pages 2330-2343

  Babarinde, Isaac Adeyemi ^a,b   Saitou, Naruya ^a,b,c  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Carnivores; Cetartiodactyls; Conserved noncoding sequences; Mammals; Primates; Rodents

Indexed keywords

SPACER DNA; UNTRANSLATED RNA;

ANIMAL; ARTICLE; ARTIODACTYLA; CARNIVORA; CARNIVORE; CATTLE; CETACEA; CETARTIODACTYLS; CLASSIFICATION; CONSERVED NONCODING SEQUENCES; DNA BASE COMPOSITION; DOG; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; RODENT; RODENTS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

CARNIVORES; CETARTIODACTYLS; CONSERVED NONCODING SEQUENCES; MAMMALS; PRIMATES; RODENTS;

ANIMALS; ARTIODACTYLA; BASE COMPOSITION; BASE SEQUENCE; CARNIVORA; CATTLE; CETACEA; CONSERVED SEQUENCE; DNA, INTERGENIC; DOGS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME; HUMANS; MICE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRIMATES; RNA, UNTRANSLATED; RODENTIA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84892554083     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt177     Document Type: Article

References (59)

1. Ahituv N, et al. 2007. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 5:9.
2. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Beck RM, Bininda-Emonds OR, Cardillo M, Liu FR, Purvis A. 2006. A higherlevel MRP supertree of plancetal mammals. BMC Evol Biol. 6:93.
4. Bejerano G, et al. 2004. Ultraconserved elements in the human genome. Science 304:1321-1325.
5. Blanga-Kanfi S, et al. 2009. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol. 9:71.
6. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15:98-110.
7. Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25-36.
8. Chen HP, et al. 2008. Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 alleledependent APOE coding region enhancer. Genomics 92:292-300.
9. Crawford GE, et al. 2006. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16:123-131.
10. Cretekos CJ, et al. 2008. Regulatory divergence modifies limb length between mammals. Genes Dev. 22:141-151.
11. Drake JA, et al. 2006. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet. 38:223-227.
12. Duret L, Dorkeld F, Gautier C. 1993. Strong conservation of noncoding sequences during vertebrates evolution: potential involvement in posttranscriptional regulation of gene expression. Nucleic Acids Res. 21: 2315-2322.
13. Elgar G. 2009. Pan-vertebrate conserved noncoding sequences associated with developmental regulation. Brief Funct Genomic Proteomic. 8: 256-265.
14. El-Kasti MM, Wells T, Carter DA. 2012. A novel long range enhancer regulates postnatal expression of Zeb2: implications for Mowat- Wilson syndrome phenotypes. Hum Mol Genet. 21:5429-5442.
15. ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
16. Frankel N, et al. 2010. Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466:490-493.
17. Graur D, et al. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 5:578-590.
18. Gupta S, et al. 2008. Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol. 4:e1000134.
19. Hardison RC. 2000. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16:369-372.
20. Hemberg M, et al. 2012. Integrated genome analysis suggests that most conserved noncoding sequences are regulatory factor binding sites. Nucleic Acids Res. 40:7858-7869.
21. Hiller M, Schaar BT, Bejerano G. 2012. Hundreds of conserved noncoding genomic regions are independently lost in mammals. Nucleic Acids Res. 40:11463-11476.
22. Janes DE, et al. 2011. Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biol Evol. 3:102-113.
23. Jones E, et al. 2011. SciPy: open source scientific tools for Python [Internet]. [cited 2011 Nov 6]. Available from: http://www.scipy.org.
24. Karro JE, Peifer M, Hardison RC, Kollmann M, von Grünberg HH. 2008. Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Mol Biol Evol. 25:362-374.
25. Katzman S, et al. 2007. Human genome ultraconserved elements are ultraselected. Science 317:915.
26. King MC, Wilson AC. 1975. Evolution at two levels in human and chimpanzees. Science 188:107-116.
27. Larkin MA, et al. 2007. 'ClustalW and ClustalX version2'. Bioinformatics 23:2947-2948.
28. Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B. 2011. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol. 28:1205-1215.
29. Lettice LA, et al. 2003. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 12:1725-1735.
30. Levy S, Hannenhalli S,Workman C. 2001. Enrichment of regulatory signals in conserved noncoding genomic sequence. Bioinformatics 17: 871-877.
31. Li W, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D. 1996. Rates of nucleotide substitution in primates and rodents and the generation- time effect hypothesis. Mol Phylogenet Evol. 5:182-187.
32. Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP. 2006. Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics 7:140.
33. Matsunami M, Saitou N. 2013. Vertebrate paralogous conserved noncoding sequences may be related to gene expression in brain. Genome Biol Evol. 5:140-150.
34. McGaughey DM, Stine ZE, Huynh JL, Vinton RM, McCallion AS. 2009. Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend. BMC Genomics 10:8
35. Meader S, Ponting CP, Lunter G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res. 20:1335-1343.
36. Meyer A, Zardoya R. 2003. Recent advances in the (molecular) phylogeny or vertebrates. Annu Rev Ecol Evol Syst. 34:311-338.
37. Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431:988-993.
38. Ovcharenko I, et al. 2005. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15:137-145.
39. Ponting CP, Hardison RC. 2011. What fraction of human genome is functional? Genome Res. 21:1769-1776.
40. R Core Team. 2013. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. [cited 2013 Mar 5]. Available from: http://www.R-project.org/.
41. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
42. Sandelin A, et al. 2004. Arrays of ultraconserved noncoding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5:99.
43. Schmidt D, et al. 2010. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor bindingdominic. Science 328: 1036-1040.
44. Shen Y, et al. 2012. A map of the cis-regulatory sequences in the mouse genome. Nature 488:116-120.
45. Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050.
46. Stern DL. 2000. Evolutionary developmental biology and the problem of variation. Evolution 54:1079-1091.
47. Takahashi M, Saitou N. 2012. Identification and characterization of lineage- specific highly conserved noncoding sequences in mammalian genomes. Genome Biol Evol. 4:641-657.
48. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
49. Thomas PD, et al. 2003. PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13:2129-2141.
50. Vavouri T, McEwen GK, Woolfe A, Gilks WR, Elgar G. 2005. Defining a genomic radius for long-range enhancer action: duplicated conserved noncoding elements hold the key. Trends Genet. 22:5-10.
51. Vavouri T,Walter K,Gilks WR, Lehner B, Elgar G. 2007. Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes fromworms to humans. Genome Biol. 8:R15.
52. Vilella AJ, et al. 2009. EnsemblComparaGeneTrees: complete, duplicationaware phylogenetic trees in vertebrates. Genome Res. 19:327-335.
53. Visel A, et al. 2009. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854-858.
54. Visel A, et al. 2013. A high-resolution enhancer atlas of the developing telencephalon. Cell 152:895-908.
55. Wittkopp PJ, Kalay G. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nature 13: 59-69.
56. Woolfe A, et al. 2004. Highly conserved noncoding sequences are associated with vertebrate development. PLoS Biol. 3:e7.
57. Wray GA. 2003. Transcriptional regulation and the evolution of development. Int J Dev Biol. 47:675-684.
58. Zhang F, Peterson T. 2006. Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.). Genetics 174(2):753-762.
59. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press. p. 97-166.