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Volumn 21, Issue 3, 2011, Pages 342-347

DNA shape, genetic codes, and evolution

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BIOLOGICAL ACTIVITY; DISEASE ASSOCIATION; DNA BASE COMPOSITION; DNA SEQUENCE; DNA SHAPE; DNA STRUCTURE; GENETIC CODE; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEOSOME; PANCREAS ISLET DISEASE; PRIORITY JOURNAL; PROTEIN CODING SEQUENCE; PROTEIN DNA INTERACTION; PROTEIN NONCODING SEQUENCE; REVIEW; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY;

EID: 79958051799     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2011.03.002     Document Type: Review
Times cited : (38)

References (54)
  • 1
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King M.C., Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 1975, 188:107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 2
    • 84968054140 scopus 로고
    • Nothing in biology makes sense except in the light of evolution
    • Dobzhansky T. Nothing in biology makes sense except in the light of evolution. Am Biol Teach 1973, 35:125-129.
    • (1973) Am Biol Teach , vol.35 , pp. 125-129
    • Dobzhansky, T.1
  • 3
    • 65249089637 scopus 로고    scopus 로고
    • Local DNA topography correlates with functional noncoding regions of the human genome
    • Parker S.C.J., Hansen L., Abaan H.O., Tullius T.D., Margulies E.H. Local DNA topography correlates with functional noncoding regions of the human genome. Science 2009, 324:389-392.
    • (2009) Science , vol.324 , pp. 389-392
    • Parker, S.C.J.1    Hansen, L.2    Abaan, H.O.3    Tullius, T.D.4    Margulies, E.H.5
  • 4
    • 34250305146 scopus 로고    scopus 로고
    • ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 5
    • 77958082013 scopus 로고    scopus 로고
    • Overlapping codes within protein-coding sequences
    • Itzkovitz S., Hodis E., Segal E. Overlapping codes within protein-coding sequences. Genome Res 2010, 20:1582-1589.
    • (2010) Genome Res , vol.20 , pp. 1582-1589
    • Itzkovitz, S.1    Hodis, E.2    Segal, E.3
  • 6
    • 45549100203 scopus 로고    scopus 로고
    • An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4
    • Lampe X., Samad O.A., Guiguen A., Matis C., Remacle S., Picard J.J., Rijli F.M., Rezsohazy R. An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Nucleic Acids Res 2008, 36:3214-3225.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3214-3225
    • Lampe, X.1    Samad, O.A.2    Guiguen, A.3    Matis, C.4    Remacle, S.5    Picard, J.J.6    Rijli, F.M.7    Rezsohazy, R.8
  • 8
    • 48249144806 scopus 로고    scopus 로고
    • A transcriptional enhancer from the coding region of ADAMTS5
    • Barthel K.K.B., Liu X. A transcriptional enhancer from the coding region of ADAMTS5. PLoS One 2008, 3:e2184.
    • (2008) PLoS One , vol.3
    • Barthel, K.K.B.1    Liu, X.2
  • 9
    • 58149512003 scopus 로고    scopus 로고
    • A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2
    • Tümpel S., Cambronero F., Sims C., Krumlauf R., Wiedemann L.M. A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc Natl Acad Sci U S A 2008, 105:20077-20082.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 20077-20082
    • Tümpel, S.1    Cambronero, F.2    Sims, C.3    Krumlauf, R.4    Wiedemann, L.M.5
  • 10
    • 53649103358 scopus 로고    scopus 로고
    • Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer
    • Chen H.P., Lin A., Bloom J.S., Khan A.H., Park C.C., Smith D.J. Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer. Genomics 2008, 92:292-300.
    • (2008) Genomics , vol.92 , pp. 292-300
    • Chen, H.P.1    Lin, A.2    Bloom, J.S.3    Khan, A.H.4    Park, C.C.5    Smith, D.J.6
  • 11
    • 0035075395 scopus 로고    scopus 로고
    • Flexibility of the genetic code with respect to DNA structure
    • Baisnée P.F., Baldi P., Brunak S., Pedersen A.G. Flexibility of the genetic code with respect to DNA structure. Bioinformatics 2001, 17:237-248.
    • (2001) Bioinformatics , vol.17 , pp. 237-248
    • Baisnée, P.F.1    Baldi, P.2    Brunak, S.3    Pedersen, A.G.4
  • 12
    • 64649095501 scopus 로고    scopus 로고
    • Nuance in the double-helix and its role in protein-DNA recognition
    • Rohs R., West S.M., Liu P., Honig B. Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol 2009, 19:171-177.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 171-177
    • Rohs, R.1    West, S.M.2    Liu, P.3    Honig, B.4
  • 13
    • 50849144848 scopus 로고    scopus 로고
    • Selective constraints in experimentally defined primate regulatory regions
    • Gaffney D.J., Blekhman R., Majewski J. Selective constraints in experimentally defined primate regulatory regions. PLoS Genet 2008, 4:e1000157.
    • (2008) PLoS Genet , vol.4
    • Gaffney, D.J.1    Blekhman, R.2    Majewski, J.3
  • 14
    • 77649278678 scopus 로고    scopus 로고
    • Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication
    • Sánchez-Gracia A., Romero-Pozuelo J., Ferrús A. Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. BMC Evol Biol 2010, 10:54.
    • (2010) BMC Evol Biol , vol.10 , pp. 54
    • Sánchez-Gracia, A.1    Romero-Pozuelo, J.2    Ferrús, A.3
  • 16
    • 79958038985 scopus 로고    scopus 로고
    • Scanning for the signatures of positive selection for human-specific insertions and deletions
    • Chen C.-H., Chuang T.-J., Liao B.-Y., Chen F.-C. Scanning for the signatures of positive selection for human-specific insertions and deletions. Genome Biol Evol 2009, 1:415-419.
    • (2009) Genome Biol Evol , vol.1 , pp. 415-419
    • Chen, C.-H.1    Chuang, T.-J.2    Liao, B.-Y.3    Chen, F.-C.4
  • 17
    • 52949123643 scopus 로고    scopus 로고
    • Insights into protein-DNA interactions through structure network analysis
    • Sathyapriya R., Vijayabaskar M.S., Vishveshwara S. Insights into protein-DNA interactions through structure network analysis. PLoS Comput Biol 2008, 4:e1000170.
    • (2008) PLoS Comput Biol , vol.4
    • Sathyapriya, R.1    Vijayabaskar, M.S.2    Vishveshwara, S.3
  • 18
    • 78149408021 scopus 로고    scopus 로고
    • Massive turnover of functional sequence in human and other mammalian genomes
    • Meader S., Ponting C.P., Lunter G. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res 2010, 20:1335-1343.
    • (2010) Genome Res , vol.20 , pp. 1335-1343
    • Meader, S.1    Ponting, C.P.2    Lunter, G.3
  • 19
    • 71749103442 scopus 로고    scopus 로고
    • Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information
    • Meireles-Filho A.C.A., Stark A. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev 2009, 19:565-570.
    • (2009) Curr Opin Genet Dev , vol.19 , pp. 565-570
    • Meireles-Filho, A.C.A.1    Stark, A.2
  • 20
    • 5144232010 scopus 로고    scopus 로고
    • A structural similarity analysis of double-helical DNA
    • Gardiner E.J., Hunter C.A., Lu X.-J., Willett P. A structural similarity analysis of double-helical DNA. J Mol Biol 2004, 343:879-889.
    • (2004) J Mol Biol , vol.343 , pp. 879-889
    • Gardiner, E.J.1    Hunter, C.A.2    Lu, X.-J.3    Willett, P.4
  • 21
    • 34250352745 scopus 로고    scopus 로고
    • Construction of a genome-scale structural map at single-nucleotide resolution
    • Greenbaum J.A., Pang B., Tullius T.D. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res 2007, 17:947-953.
    • (2007) Genome Res , vol.17 , pp. 947-953
    • Greenbaum, J.A.1    Pang, B.2    Tullius, T.D.3
  • 24
    • 77950934795 scopus 로고    scopus 로고
    • The shape of the DNA minor groove directs binding by the DNA-bending protein Fis
    • Stella S., Cascio D., Johnson R.C. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev 2010, 24:814-826.
    • (2010) Genes Dev , vol.24 , pp. 814-826
    • Stella, S.1    Cascio, D.2    Johnson, R.C.3
  • 25
  • 26
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li W.H., Wu C.I., Luo C.C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 1985, 2:150-174.
    • (1985) Mol Biol Evol , vol.2 , pp. 150-174
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 27
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: advances through genomics
    • Jiang C., Pugh B.F. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2010, 10:161-172.
    • (2010) Nat Rev Genet , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 28
    • 76949093375 scopus 로고    scopus 로고
    • Nucleosome positioning: how is it established, and why does it matter?
    • Radman-Livaja M., Rando O.J. Nucleosome positioning: how is it established, and why does it matter?. Dev Biol 2010, 339:258-266.
    • (2010) Dev Biol , vol.339 , pp. 258-266
    • Radman-Livaja, M.1    Rando, O.J.2
  • 29
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal E., Widom J. What controls nucleosome positions?. Trends Genet 2009, 25:335-343.
    • (2009) Trends Genet , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 30
    • 33749153628 scopus 로고    scopus 로고
    • Nucleosome positions predicted through comparative genomics
    • Ioshikhes I.P., Albert I., Zanton S.J., Pugh B.F. Nucleosome positions predicted through comparative genomics. Nat Genet 2006, 38:1210-1215.
    • (2006) Nat Genet , vol.38 , pp. 1210-1215
    • Ioshikhes, I.P.1    Albert, I.2    Zanton, S.J.3    Pugh, B.F.4
  • 32
    • 34447644439 scopus 로고    scopus 로고
    • A novel 'roll-and-slide' mechanism of DNA folding in chromatin: Implications for nucleosome positioning
    • Tolstorukov M.Y., Colasanti A.V., McCandlish D.M., Olson W.K., Zhurkin V.B. A novel 'roll-and-slide' mechanism of DNA folding in chromatin: Implications for nucleosome positioning. J Mol Biol 2007, 371:725-738.
    • (2007) J Mol Biol , vol.371 , pp. 725-738
    • Tolstorukov, M.Y.1    Colasanti, A.V.2    McCandlish, D.M.3    Olson, W.K.4    Zhurkin, V.B.5
  • 33
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo D., Hughes T.R. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinform 2009, 10:442.
    • (2009) BMC Bioinform , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 34
    • 74949115966 scopus 로고    scopus 로고
    • Chromatin 'programming' by sequence-is there more to the nucleosome code than %GC?
    • Hughes A., Rando O.J. Chromatin 'programming' by sequence-is there more to the nucleosome code than %GC?. J Biol 2009, 8:96.
    • (2009) J Biol , vol.8 , pp. 96
    • Hughes, A.1    Rando, O.J.2
  • 35
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: major determinants of nucleosome organization
    • Segal E., Widom J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 2009, 19:65-71.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 36
    • 78651343432 scopus 로고    scopus 로고
    • Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae
    • Sugihara F., Kasahara K., Kokubo T. Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. Nucleic Acids Res 2011, 39:59-75.
    • (2011) Nucleic Acids Res , vol.39 , pp. 59-75
    • Sugihara, F.1    Kasahara, K.2    Kokubo, T.3
  • 38
    • 47649094814 scopus 로고    scopus 로고
    • Inferring natural selection on fine-scale chromatin organization in yeast
    • Babbitt G.A., Kim Y. Inferring natural selection on fine-scale chromatin organization in yeast. Mol Biol Evol 2008, 25:1714-1727.
    • (2008) Mol Biol Evol , vol.25 , pp. 1714-1727
    • Babbitt, G.A.1    Kim, Y.2
  • 39
    • 77953296396 scopus 로고    scopus 로고
    • The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer
    • Babbitt G.A., Tolstorukov M.Y., Kim Y. The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer. J Biomol Struct Dyn 2010, 27:765-780.
    • (2010) J Biomol Struct Dyn , vol.27 , pp. 765-780
    • Babbitt, G.A.1    Tolstorukov, M.Y.2    Kim, Y.3
  • 40
    • 78651240895 scopus 로고    scopus 로고
    • Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast
    • Kenigsberg E., Bar A., Segal E., Tanay A. Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol 2010, 6:e1001039.
    • (2010) PLoS Comput Biol , vol.6
    • Kenigsberg, E.1    Bar, A.2    Segal, E.3    Tanay, A.4
  • 41
    • 79952255486 scopus 로고    scopus 로고
    • Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes
    • Babbitt G.A., Cotter C.R. Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes. Genome Biol Evol 2011, 3:15-22.
    • (2011) Genome Biol Evol , vol.3 , pp. 15-22
    • Babbitt, G.A.1    Cotter, C.R.2
  • 42
    • 71049147904 scopus 로고    scopus 로고
    • The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes
    • Cohanim A.B., Haran T.E. The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes. Nucleic Acids Res 2009, 37:6466-6476.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6466-6476
    • Cohanim, A.B.1    Haran, T.E.2
  • 44
    • 77952786822 scopus 로고    scopus 로고
    • Genomic medicine-an updated primer
    • Feero W.G., Guttmacher A.E., Collins F.S. Genomic medicine-an updated primer. NEJM 2010, 362:2001-2011.
    • (2010) NEJM , vol.362 , pp. 2001-2011
    • Feero, W.G.1    Guttmacher, A.E.2    Collins, F.S.3
  • 48
    • 78650499829 scopus 로고    scopus 로고
    • Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs
    • Petrie K.L., Joyce G.F. Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs. Nucleic Acids Res 2010, 38:8095-8104.
    • (2010) Nucleic Acids Res , vol.38 , pp. 8095-8104
    • Petrie, K.L.1    Joyce, G.F.2
  • 50
    • 78650331647 scopus 로고    scopus 로고
    • modENCODE Consortium Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • modENCODE Consortium Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797.
    • (2010) Science , vol.330 , pp. 1787-1797
  • 51
    • 75149143994 scopus 로고    scopus 로고
    • Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
    • Weirauch M.T., Hughes T.R. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet 2010, 26:66-74.
    • (2010) Trends Genet , vol.26 , pp. 66-74
    • Weirauch, M.T.1    Hughes, T.R.2
  • 54
    • 70349866695 scopus 로고    scopus 로고
    • Upcoming challenges for multiple sequence alignment methods in the high-throughput era
    • Kemena C., Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 2009, 25:2455-2465.
    • (2009) Bioinformatics , vol.25 , pp. 2455-2465
    • Kemena, C.1    Notredame, C.2


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