Functional evolution of noncoding DNA.

Noncoding DNA in eukaryotes encodes functionally important signals for the regulation of chromosome assembly, DNA replication, and gene expression. The increasing availability of whole-genome sequences of related taxa has led to interest in the evolution of these signals, and the phylogenetic footprints they produce. Cis-regulatory sequences controlling gene expression are often conserved among related species, but are rarely conserved between distantly related taxa. Several experimentally characterized regulatory elements have failed to show sequence similarity even between closely related species.

[1]  M. Kimura,et al.  Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[2]  D. Stern.  PERSPECTIVE: EVOLUTIONARY DEVELOPMENTAL BIOLOGY AND THE PROBLEM OF VARIATION , 2000, Evolution; international journal of organic evolution.

[3]  V. B. Yap,et al.  Association between divergence and interspersed repeats in mammalian noncoding genomic DNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[4]  W. Wasserman,et al.  A predictive model for regulatory sequences directing liver-specific transcription. , 2001, Genome research.

[5]  N. Patel,et al.  Evidence for stabilizing selection in a eukaryotic enhancer element , 2000, Nature.

[6]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[7]  G. K. Wong,et al.  Is "junk" DNA mostly intron DNA? , 2000, Genome research.

[8]  J. Kim.  Macro-evolution of the hairy enhancer in Drosophila species. , 2001, The Journal of experimental zoology.

[9]  M. Long,et al.  Evolution of novel genes. , 2001, Current opinion in genetics & development.

[10]  Terence Hwa,et al.  On the Selection and Evolution of Regulatory DNA Motifs , 2001, Journal of Molecular Evolution.

[11]  E. Davidson,et al.  The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.

[12]  F. Müller,et al.  Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  S. Eddy.  Computational Genomics of Noncoding RNA Genes , 2002, Cell.

[14]  N. Satoh,et al.  Evolutionary alterations of the minimal promoter for notochord-specific Brachyury expression in ascidian embryos. , 1999, Development.

[15]  W. Herr,et al.  The SV40 enhancer contains two distinct levels of organization , 1988, Nature.

[16]  M A Koch,et al.  Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. , 2001, Molecular biology and evolution.

[17]  D. Tautz.  Evolution of transcriptional regulation. , 2000, Current opinion in genetics & development.

[18]  S. Carroll,et al.  From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design , 2000 .

[19]  R. Durbin,et al.  Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. , 1999, Genome research.

[20]  P. Bucher,et al.  Searching for regulatory elements in human noncoding sequences. , 1997, Current opinion in structural biology.

[21]  W. Miller,et al.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. , 2000, Science.

[22]  S Schwartz,et al.  Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes. , 1991, Journal of molecular biology.

[23]  M. Levine,et al.  Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. , 1991, Science.

[24]  S. Shabalina,et al.  Pattern of selective constraint in C. elegans and C. briggsae genomes. , 1999, Genetical research.

[25]  A. Clark,et al.  Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. , 2002, Molecular biology and evolution.

[26]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[27]  Eleanor Lawrence,et al.  The encyclopedia of molecular biology , 1995 .

[28]  Alexey S Kondrashov,et al.  Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. , 2002, Nucleic acids research.

[29]  William McGinnis,et al.  Hox protein mutation and macroevolution of the insect body plan , 2002, Nature.

[30]  M. Levine,et al.  Short-range transcriptional repressors mediate both quenching and direct repression within complex loci in Drosophila. , 1996, Genes & development.

[31]  D. Crawford,et al.  Functional Analyses of Natural Variation in Sp1 Binding Sites of a TATA-Less Promoter , 1999, Journal of Molecular Evolution.

[32]  PERSPECTIVE: EVOLUTIONARY DEVELOPMENTAL BIOLOGY AND THE PROBLEM OF VARIATION , 2000 .

[33]  S. Carroll,et al.  Hox repression of a target gene: extradenticle-independent, additive action through multiple monomer binding sites. , 2002, Development.

[34]  R. Hardison.  Conserved noncoding sequences are reliable guides to regulatory elements. , 2000, Trends in genetics : TIG.

[35]  J. T. Kadonaga,et al.  Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. , 2001, Genes & development.

[36]  John M. Hancock,et al.  Rapid restructuring of bicoid‐dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution , 2001, Evolution & development.

[37]  T. Maniatis,et al.  A conserved regulatory unit implicated in tissue-specific gene expression in Drosophila and man. , 1992, Genes & development.

[38]  Ken Dewar,et al.  Molecular evolution of the HoxA cluster in the three major gnathostome lineages , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[39]  J. Fickett,et al.  Discovery and modeling of transcriptional regulatory regions. , 2000, Current opinion in biotechnology.

[40]  A. Carter,et al.  Evolution of functionally conserved enhancers can be accelerated in large populations: a population–genetic model , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[41]  M. Levine,et al.  Related target enhancers for dorsal and NF-kappa B signaling pathways. , 1994, Science.

[42]  L. Pennacchio,et al.  Genomic strategies to identify mammalian regulatory sequences , 2001, Nature Reviews Genetics.

[43]  Jody Hey,et al.  The limits of selection during maize domestication , 1999, Nature.

[44]  M. Levine,et al.  hairy mediates dominant repression in the Drosophila embryo , 1997, The EMBO journal.

[45]  M. Kreitman,et al.  Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. , 2001, Genome research.

[46]  Sean B. Carroll,et al.  Evolution of a transcriptional repression domain in an insect Hox protein , 2002, Nature.

[47]  T. Maniatis,et al.  A Drosophila CREB/ATF transcriptional activator binds to both fat body- and liver-specific regulatory elements. , 1992, Genes & development.

[48]  J. Stone,et al.  Rapid evolution of cis-regulatory sequences via local point mutations. , 2001, Molecular biology and evolution.

[49]  N. Patel,et al.  Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. , 1998, Development.

[50]  D. Stern,et al.  Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. , 2000, Proceedings of the National Academy of Sciences of the United States of America.