메뉴 건너뛰기




Volumn 9, Issue 1-2, 2011, Pages 1-6

Thirty years of multiple sequence codes

Author keywords

Chromatin code; Code degeneracy; Code interaction; Genomic code; Second genetic code

Indexed keywords

DNA; HISTONE;

EID: 79957902393     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/S1672-0229(11)60001-6     Document Type: Review
Times cited : (18)

References (47)
  • 1
    • 0018894384 scopus 로고
    • Selfish genes, the phenotype paradigm and genome evolution
    • Doolittle W.F., Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature 1980, 284:601-603.
    • (1980) Nature , vol.284 , pp. 601-603
    • Doolittle, W.F.1    Sapienza, C.2
  • 2
    • 0018857680 scopus 로고
    • Selfish DNA: the ultimate parasite
    • Orgel L.E., Crick F.H. Selfish DNA: the ultimate parasite. Nature 1980, 284:604-607.
    • (1980) Nature , vol.284 , pp. 604-607
    • Orgel, L.E.1    Crick, F.H.2
  • 3
    • 0002551496 scopus 로고
    • Genetic recombination in fungi
    • Australian Academy of Science, Canberra, Australia, W.J. Peacock, R.D. Brock (Eds.)
    • Holliday R. Genetic recombination in fungi. Replication and Recombination of Genetic Material 1968, 157-174. Australian Academy of Science, Canberra, Australia. W.J. Peacock, R.D. Brock (Eds.).
    • (1968) Replication and Recombination of Genetic Material , pp. 157-174
    • Holliday, R.1
  • 4
    • 0015895045 scopus 로고
    • An analysis of the bovine genome by Cs2SO4-Ag+ density gradient centrifugation
    • Filipski J., et al. An analysis of the bovine genome by Cs2SO4-Ag+ density gradient centrifugation. J. Mol. Biol. 1973, 80:177-197.
    • (1973) J. Mol. Biol. , vol.80 , pp. 177-197
    • Filipski, J.1
  • 5
    • 0025087316 scopus 로고
    • Le génomes des vertébrés: organization, fonction et evolution
    • Bernardi G. Le génomes des vertébrés: organization, fonction et evolution. Biofutur 1990, 94:43-46.
    • (1990) Biofutur , vol.94 , pp. 43-46
    • Bernardi, G.1
  • 6
    • 0019322507 scopus 로고
    • Sequence-dependent deformational anisotropy of chromatin DNA
    • Trifonov E.N. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 1980, 8:4041-4053.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 4041-4053
    • Trifonov, E.N.1
  • 7
    • 0039581268 scopus 로고
    • Structure of DNA in chromatin
    • Springer, Berlin, Germany, H. Schweiger (Ed.)
    • Trifonov E.N. Structure of DNA in chromatin. International Cell Biology 1980-1981 1981, 128-138. Springer, Berlin, Germany. H. Schweiger (Ed.).
    • (1981) International Cell Biology 1980-1981 , pp. 128-138
    • Trifonov, E.N.1
  • 8
    • 79957898942 scopus 로고
    • Second genetic code deciphered, solving a protein synthesis puzzle. New York Times May 13.
    • Kolata, G. 1988. Second genetic code deciphered, solving a protein synthesis puzzle. New York Times May 13.
    • (1988)
    • Kolata, G.1
  • 9
    • 0024284965 scopus 로고
    • A simple structural feature is a major determinant of the identity of a transfer RNA
    • Hou Y.M., Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 1988, 333:140-145.
    • (1988) Nature , vol.333 , pp. 140-145
    • Hou, Y.M.1    Schimmel, P.2
  • 10
    • 0018872571 scopus 로고
    • Are snRNPs involved in splicing?
    • Lerner M.R., et al. Are snRNPs involved in splicing?. Nature 1980, 283:220-224.
    • (1980) Nature , vol.283 , pp. 220-224
    • Lerner, M.R.1
  • 11
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • Eddy S.R. Non-coding RNA genes and the modern RNA world. Nature Rev. Genet. 2001, 2:919-929.
    • (2001) Nature Rev. Genet. , vol.2 , pp. 919-929
    • Eddy, S.R.1
  • 13
    • 79957925696 scopus 로고    scopus 로고
    • Packaging proteins may be second genetic code. New Scientist August 9.
    • Young, E. 2001. Packaging proteins may be second genetic code. New Scientist August 9.
    • (2001)
    • Young, E.1
  • 14
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • Jenuwein T., Allis C.D. Translating the histone code. Science 2001, 293:1074-1080.
    • (2001) Science , vol.293 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 15
    • 79957889707 scopus 로고    scopus 로고
    • Scientists say they've found a code beyond genetics in DNA. New York Times July 25.
    • Wade, N. 2006. Scientists say they've found a code beyond genetics in DNA. New York Times July 25.
    • (2006)
    • Wade, N.1
  • 16
    • 33747500567 scopus 로고    scopus 로고
    • A genomic code for nucleosome positioning
    • Segal E., et al. A genomic code for nucleosome positioning. Nature 2006, 442:772-778.
    • (2006) Nature , vol.442 , pp. 772-778
    • Segal, E.1
  • 17
    • 79957918876 scopus 로고    scopus 로고
    • Cracking the second genetic code
    • Hughes T. Cracking the second genetic code. FASEB J. 2008, 22:262.2.
    • (2008) FASEB J. , vol.22
    • Hughes, T.1
  • 18
    • 77952081349 scopus 로고    scopus 로고
    • Gene regulation: breaking the second genetic code
    • Tejedor J.R., Valcárcel J. Gene regulation: breaking the second genetic code. Nature 2010, 465:45-46.
    • (2010) Nature , vol.465 , pp. 45-46
    • Tejedor, J.R.1    Valcárcel, J.2
  • 19
    • 77952029221 scopus 로고    scopus 로고
    • Deciphering the splicing code
    • Barash Y., et al. Deciphering the splicing code. Nature 2010, 465:53-59.
    • (2010) Nature , vol.465 , pp. 53-59
    • Barash, Y.1
  • 20
    • 79957917151 scopus 로고    scopus 로고
    • FinchTalk. Journal Club May 11.
    • Smith, T. 2010. FinchTalk. Journal Club May 11.
    • (2010)
    • Smith, T.1
  • 21
    • 0019363396 scopus 로고
    • Organization and expression of eukaryotic split genes coding for proteins
    • Breathnach R., Chambon P. Organization and expression of eukaryotic split genes coding for proteins. Annu. Rev. Biochem. 1981, 50:349-383.
    • (1981) Annu. Rev. Biochem. , vol.50 , pp. 349-383
    • Breathnach, R.1    Chambon, P.2
  • 22
    • 0024334889 scopus 로고
    • The multiple codes of nucleotide sequences
    • Trifonov E.N. The multiple codes of nucleotide sequences. Bull. Math. Biol. 1989, 51:417-432.
    • (1989) Bull. Math. Biol. , vol.51 , pp. 417-432
    • Trifonov, E.N.1
  • 23
    • 0030474941 scopus 로고    scopus 로고
    • Interfering contexts of regulatory sequence elements
    • Trifonov E.N. Interfering contexts of regulatory sequence elements. Comput. Appl. Biosci. 1996, 12:423-429.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 423-429
    • Trifonov, E.N.1
  • 24
    • 0347206613 scopus 로고    scopus 로고
    • Sequence codes
    • John Wiley & Sons, New York, USA, T.E. Creighton (Ed.)
    • Trifonov E.N. Sequence codes. Encyclopedia of Molecular Biology 1999, 2324-2326. John Wiley & Sons, New York, USA. T.E. Creighton (Ed.).
    • (1999) Encyclopedia of Molecular Biology , pp. 2324-2326
    • Trifonov, E.N.1
  • 25
    • 60849116141 scopus 로고    scopus 로고
    • Nucleosome DNA bendability matrix (C. elegans)
    • Gabdank I., et al. Nucleosome DNA bendability matrix (C. elegans). J. Biomol. Struct. Dyn. 2009, 26:403-411.
    • (2009) J. Biomol. Struct. Dyn. , vol.26 , pp. 403-411
    • Gabdank, I.1
  • 26
    • 76749140862 scopus 로고    scopus 로고
    • Base pair stacking in nucleosome DNA and bendability sequence pattern
    • Trifonov E.N. Base pair stacking in nucleosome DNA and bendability sequence pattern. J. Theor. Biol. 2010, 263:337-339.
    • (2010) J. Theor. Biol. , vol.263 , pp. 337-339
    • Trifonov, E.N.1
  • 27
    • 77951969370 scopus 로고    scopus 로고
    • Nucleosome positioning by sequence, state of the art and apparent finale
    • Trifonov E.N. Nucleosome positioning by sequence, state of the art and apparent finale. J. Biomol. Struct. Dyn. 2010, 27:741-746.
    • (2010) J. Biomol. Struct. Dyn. , vol.27 , pp. 741-746
    • Trifonov, E.N.1
  • 28
    • 78650937771 scopus 로고    scopus 로고
    • Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences
    • Rapoport A.E., et al. Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J. Biomol. Struct. Dyn. 2011, 28:567-574.
    • (2011) J. Biomol. Struct. Dyn. , vol.28 , pp. 567-574
    • Rapoport, A.E.1
  • 29
    • 33845298285 scopus 로고    scopus 로고
    • Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
    • Johnson S.M., et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006, 16:1505-1516.
    • (2006) Genome Res. , vol.16 , pp. 1505-1516
    • Johnson, S.M.1
  • 30
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide sequence
    • Trifonov E.N., Sussman J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 1980, 77:3816-3820.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 31
    • 0021100990 scopus 로고
    • Nucleotide sequence-directed mapping of the nucleosomes
    • Mengeritsky G., Trifonov E.N. Nucleotide sequence-directed mapping of the nucleosomes. Nucleic Acids Res. 1983, 11:3833-3851.
    • (1983) Nucleic Acids Res. , vol.11 , pp. 3833-3851
    • Mengeritsky, G.1    Trifonov, E.N.2
  • 32
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S.C., et al. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 1986, 191:659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1
  • 33
    • 0029317241 scopus 로고
    • CC dinucleotides contribute to the bending of DNA in chromatin
    • Bolshoy A. CC dinucleotides contribute to the bending of DNA in chromatin. Nat. Struct. Biol. 1995, 2:446-448.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 446-448
    • Bolshoy, A.1
  • 34
    • 0023777538 scopus 로고
    • Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism
    • Kornberg R.D., Stryer L. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 1988, 16:6677-6690.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 6677-6690
    • Kornberg, R.D.1    Stryer, L.2
  • 35
    • 36349006915 scopus 로고    scopus 로고
    • Experiments confirm the influence of genome long-range correlations on nucleosome positioning
    • Vaillant C., et al. Experiments confirm the influence of genome long-range correlations on nucleosome positioning. Phys. Rev. Lett. 2007, 99:218103.
    • (2007) Phys. Rev. Lett. , vol.99 , pp. 218103
    • Vaillant, C.1
  • 36
    • 70449591286 scopus 로고    scopus 로고
    • Repertoires of the nucleosome-positioning dinucleotides
    • Bettecken T., Trifonov E.N. Repertoires of the nucleosome-positioning dinucleotides. PLoS One 2009, 4:e7654.
    • (2009) PLoS One , vol.4
    • Bettecken, T.1    Trifonov, E.N.2
  • 37
    • 47849088254 scopus 로고    scopus 로고
    • Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element
    • Salih F., et al. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J. Biomol. Struct. Dyn. 2008, 26:9-16.
    • (2008) J. Biomol. Struct. Dyn. , vol.26 , pp. 9-16
    • Salih, F.1
  • 38
    • 77956510995 scopus 로고    scopus 로고
    • Single-base resolution nucleosome mapping on DNA sequences
    • Gabdank I., et al. Single-base resolution nucleosome mapping on DNA sequences. J. Biomol. Struct. Dyn. 2010, 28:107-122.
    • (2010) J. Biomol. Struct. Dyn. , vol.28 , pp. 107-122
    • Gabdank, I.1
  • 39
    • 77951944594 scopus 로고    scopus 로고
    • FineStr: a web server for single-base-resolution nucleosome positioning
    • Gabdank I., et al. FineStr: a web server for single-base-resolution nucleosome positioning. Bioinformatics 2010, 26:845-846.
    • (2010) Bioinformatics , vol.26 , pp. 845-846
    • Gabdank, I.1
  • 40
    • 34447644439 scopus 로고    scopus 로고
    • A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning
    • Tolstorukov M.Y., et al. 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
  • 41
    • 77953295415 scopus 로고    scopus 로고
    • Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro
    • Cui F., Zhurkin V.B. Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro. J. Biomol. Struct. Dyn. 2010, 27:821-841.
    • (2010) J. Biomol. Struct. Dyn. , vol.27 , pp. 821-841
    • Cui, F.1    Zhurkin, V.B.2
  • 42
    • 77953304067 scopus 로고    scopus 로고
    • Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove
    • Wang D., et al. Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove. J. Biomol. Struct. Dyn. 2010, 27:843-859.
    • (2010) J. Biomol. Struct. Dyn. , vol.27 , pp. 843-859
    • Wang, D.1
  • 43
    • 0033884290 scopus 로고    scopus 로고
    • Optimization of nucleic acid sequences
    • Lafontaine I., Lavery R. Optimization of nucleic acid sequences. Biophys. J. 2000, 79:680-685.
    • (2000) Biophys. J. , vol.79 , pp. 680-685
    • Lafontaine, I.1    Lavery, R.2
  • 44
    • 0022527052 scopus 로고
    • Sequence-directed curvature of DNA
    • Hagerman P.J. Sequence-directed curvature of DNA. Nature 1986, 321:449-450.
    • (1986) Nature , vol.321 , pp. 449-450
    • Hagerman, P.J.1
  • 45
    • 0024121469 scopus 로고
    • Calibration of DNA curvature and a unified description of sequence-directed bending
    • Koo H.S., Crothers D.M. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl. Acad. Sci. USA 1988, 85:1763-1767.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 1763-1767
    • Koo, H.S.1    Crothers, D.M.2
  • 46
    • 0026089491 scopus 로고
    • Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles
    • Bolshoy A., et al. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 1991, 88:2312-2316.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 2312-2316
    • Bolshoy, A.1
  • 47
    • 79957919134 scopus 로고    scopus 로고
    • Protective rotational positioning of splice junctions in nucleosomes. In Abstracts of Alternative Splicing-Special Interest Group Meeting, Boston, USA.
    • Hapala, J., Trifonov, E.N. 2010. Protective rotational positioning of splice junctions in nucleosomes. In Abstracts of Alternative Splicing-Special Interest Group Meeting, pp. 51. Boston, USA.
    • (2010) , pp. 51
    • Hapala, J.1    Trifonov, E.N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.