메뉴 건너뛰기




Volumn 343, Issue 4, 2004, Pages 891-901

Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA

Author keywords

DNA supercoiling; genomes; nucleosomes; sequence periodicities; thermophilicity

Indexed keywords

DINUCLEOTIDE; DNA; GENOMIC DNA; NUCLEOTIDE;

EID: 5144227142     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.08.068     Document Type: Article
Times cited : (44)

References (41)
  • 1
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide sequence
    • E. Trifonov, and J. Sussman The pitch of chromatin DNA is reflected in its nucleotide sequence Proc. Natl Acad. Sci. USA 77 1980 3816 3820
    • (1980) Proc. Natl Acad. Sci. USA , vol.77 , pp. 3816-3820
    • Trifonov, E.1    Sussman, J.2
  • 2
    • 0033379115 scopus 로고    scopus 로고
    • DNA repeats archaeal nucleosome positioning
    • K. Bailey, and J. Reeve DNA repeats archaeal nucleosome positioning Res. Microbiol. 150 1999 701 709
    • (1999) Res. Microbiol. , vol.150 , pp. 701-709
    • Bailey, K.1    Reeve, J.2
  • 3
    • 0031757877 scopus 로고    scopus 로고
    • Sequence periodicity in complete genomes of archaea suggests positive supercoiling
    • H. Herzel, O. Weiss, and E. Trifonov Sequence periodicity in complete genomes of archaea suggests positive supercoiling J. Biomol. Struct. Dynam. 16 1998 341 345
    • (1998) J. Biomol. Struct. Dynam. , vol.16 , pp. 341-345
    • Herzel, H.1    Weiss, O.2    Trifonov, E.3
  • 4
    • 0030596486 scopus 로고    scopus 로고
    • Short-range order in two eukaryotic genomes: Relation to chromosome structure
    • J. Widom Short-range order in two eukaryotic genomes: relation to chromosome structure J. Mol. Biol. 259 1996 579 588
    • (1996) J. Mol. Biol. , vol.259 , pp. 579-588
    • Widom, J.1
  • 5
    • 0032891716 scopus 로고    scopus 로고
    • 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
    • H. Herzel, O. Weiss, and E. Trifonov 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding Bioinformatics 15 1999 187 193
    • (1999) Bioinformatics , vol.15 , pp. 187-193
    • Herzel, H.1    Weiss, O.2    Trifonov, E.3
  • 6
    • 0032770571 scopus 로고    scopus 로고
    • ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes
    • M. Tomita, M. Wada, and Y. Kawashima ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes J. Mol. Evol. 49 1999 182 192
    • (1999) J. Mol. Evol. , vol.49 , pp. 182-192
    • Tomita, M.1    Wada, M.2    Kawashima, Y.3
  • 7
    • 0034141421 scopus 로고    scopus 로고
    • Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima
    • P. Worning, L. Jensen, K. Nelson, S. Brunak, and D. Ussery Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima Nucl. Acids Res. 28 2000 706 709
    • (2000) Nucl. Acids Res. , vol.28 , pp. 706-709
    • Worning, P.1    Jensen, L.2    Nelson, K.3    Brunak, S.4    Ussery, D.5
  • 10
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • K. Luger, A. Mader, R. Richmond, D. Sargent, and T. Richmond Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.2    Richmond, R.3    Sargent, D.4    Richmond, T.5
  • 11
    • 0021154312 scopus 로고
    • Reverse gyrase - A topoisomerase which introduces positive superhelical turns into DNA
    • A. Kikuchi, and K. Asai Reverse gyrase - a topoisomerase which introduces positive superhelical turns into DNA Nature 309 1984 677 681
    • (1984) Nature , vol.309 , pp. 677-681
    • Kikuchi, A.1    Asai, K.2
  • 12
    • 0025885691 scopus 로고
    • DNA binding by the archaeal histone HMf results in positive supercoiling
    • D. Musgrave, K. Sandman, and J. Reeve DNA binding by the archaeal histone HMf results in positive supercoiling Proc. Natl Acad. Sci. USA 88 1991 10397 10401
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 10397-10401
    • Musgrave, D.1    Sandman, K.2    Reeve, J.3
  • 13
    • 0030956537 scopus 로고    scopus 로고
    • DNA topology in hyperthermophilic archaea: Reference states and their variation with growth phase, growth temperature, and temperature stresses
    • P. Lopez-Garcia, and P. Forterre DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses Mol. Microbiol. 23 1997 1267 1279
    • (1997) Mol. Microbiol. , vol.23 , pp. 1267-1279
    • Lopez-Garcia, P.1    Forterre, P.2
  • 14
    • 0022449038 scopus 로고
    • Positively supercoiled DNA in a virus-like particle of an archaebacterium
    • M. Nadal, G. Mirambeau, P. Forterre, W.-D. Reiter, and M. Duguet Positively supercoiled DNA in a virus-like particle of an archaebacterium Nature 321 1986 256 258
    • (1986) Nature , vol.321 , pp. 256-258
    • Nadal, M.1    Mirambeau, G.2    Forterre, P.3    Reiter, W.-D.4    Duguet, M.5
  • 16
    • 0033980483 scopus 로고    scopus 로고
    • Negative constrained DNA supercoiling in archaeal nucleosomes
    • D. Musgrave, P. Forterre, and A. Slesarev Negative constrained DNA supercoiling in archaeal nucleosomes Mol. Microbiol. 35 2000 341 349
    • (2000) Mol. Microbiol. , vol.35 , pp. 341-349
    • Musgrave, D.1    Forterre, P.2    Slesarev, A.3
  • 17
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • S. Satchwell, H. Drew, and A. Travers Sequence periodicities in chicken nucleosome core DNA J. Mol. Biol. 191 1986 659 675
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.1    Drew, H.2    Travers, A.3
  • 18
    • 0030595138 scopus 로고    scopus 로고
    • Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
    • I. Ioshikhes, A. Bolshoy, K. Derenshteyn, M. Borodovsky, and E. Trifonov Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences J. Mol. Biol. 262 1996 129 139
    • (1996) J. Mol. Biol. , vol.262 , pp. 129-139
    • Ioshikhes, I.1    Bolshoy, A.2    Derenshteyn, K.3    Borodovsky, M.4    Trifonov, E.5
  • 19
    • 0001079085 scopus 로고
    • Artificial nucleosome positioning sequences
    • T. Shrader, and D. Crothers Artificial nucleosome positioning sequences Proc. Natl Acad. Sci. USA 86 1989 7418 7422
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 7418-7422
    • Shrader, T.1    Crothers, D.2
  • 20
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
    • A. Thastrom, P. Lowary, H. Widlund, H. Cao, M. Kubista, and J. Widom Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences J. Mol. Biol. 288 1999 213 229
    • (1999) J. Mol. Biol. , vol.288 , pp. 213-229
    • Thastrom, A.1    Lowary, P.2    Widlund, H.3    Cao, H.4    Kubista, M.5    Widom, J.6
  • 21
    • 0034644767 scopus 로고    scopus 로고
    • Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution
    • K. Bailey, S. Pereira, J. Widom, and J. Reeve Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution J. Mol. Biol. 303 2000 25 34
    • (2000) J. Mol. Biol. , vol.303 , pp. 25-34
    • Bailey, K.1    Pereira, S.2    Widom, J.3    Reeve, J.4
  • 22
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • J. Garnier, D. Osguthorpe, and B. Robson Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins J. Mol. Biol. 120 1978 97 120
    • (1978) J. Mol. Biol. , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.2    Robson, B.3
  • 23
    • 0019065166 scopus 로고
    • Local hydrophobicity stabilizes secondary structures in proteins
    • M. Kanehisa, and T. Tsong Local hydrophobicity stabilizes secondary structures in proteins Biopolymers 19 1980 1617 1628
    • (1980) Biopolymers , vol.19 , pp. 1617-1628
    • Kanehisa, M.1    Tsong, T.2
  • 24
    • 0029115481 scopus 로고
    • A sequence property approach to searching protein databases
    • U. Hobohm, and C. Sander A sequence property approach to searching protein databases J. Mol. Biol. 251 1995 390 399
    • (1995) J. Mol. Biol. , vol.251 , pp. 390-399
    • Hobohm, U.1    Sander, C.2
  • 26
    • 0019887286 scopus 로고
    • Periodicity in DNA primary structure is defined by secondary structure of the coded protein
    • V. Zhurkin Periodicity in DNA primary structure is defined by secondary structure of the coded protein Nucl. Acids Res. 9 1981 1963 1971
    • (1981) Nucl. Acids Res. , vol.9 , pp. 1963-1971
    • Zhurkin, V.1
  • 27
    • 0032554318 scopus 로고    scopus 로고
    • Correlations in protein sequences and property codes
    • O. Weiss, and H. Herzel Correlations in protein sequences and property codes J. Theoret. Biol. 190 1998 341 353
    • (1998) J. Theoret. Biol. , vol.190 , pp. 341-353
    • Weiss, O.1    Herzel, H.2
  • 31
    • 0030479536 scopus 로고    scopus 로고
    • The origin of interspersed repeats in the human genome
    • A. Smit The origin of interspersed repeats in the human genome Curr. Opin. Genet. Dev. 6 1996 743 748
    • (1996) Curr. Opin. Genet. Dev. , vol.6 , pp. 743-748
    • Smit, A.1
  • 32
    • 0037178777 scopus 로고    scopus 로고
    • Modifying gene expression programs by altering core promoter chromatin architecture
    • S. Lomvardas, and D. Thanos Modifying gene expression programs by altering core promoter chromatin architecture Cell 110 2002 261 271
    • (2002) Cell , vol.110 , pp. 261-271
    • Lomvardas, S.1    Thanos, D.2
  • 33
    • 0032001782 scopus 로고    scopus 로고
    • Interpreting correlations in biosequences
    • H. Herzel, E. Trifonov, O. Weiss, and I. Grosse Interpreting correlations in biosequences Physica A 249 1998 449 459
    • (1998) Physica a , vol.249 , pp. 449-459
    • Herzel, H.1    Trifonov, E.2    Weiss, O.3    Grosse, I.4
  • 34
    • 0029833881 scopus 로고    scopus 로고
    • Isolation and chromosomal distribution of natural Z-DNA-forming sequences in Halobacterium halobium
    • J. Kim, and S. DasSarma Isolation and chromosomal distribution of natural Z-DNA-forming sequences in Halobacterium halobium J. Biol. Chem. 271 1996 19724 19731
    • (1996) J. Biol. Chem. , vol.271 , pp. 19724-19731
    • Kim, J.1    Dassarma, S.2
  • 35
    • 0030043986 scopus 로고    scopus 로고
    • Genetic and topological analyses of the bop promoter of Halobacterium halobium: Stimulation by DNA supercoiling and non-B-DNA structure
    • C. Yang, J. Kim, E. Molinari, and S. DasSarma Genetic and topological analyses of the bop promoter of Halobacterium halobium: stimulation by DNA supercoiling and non-B-DNA structure J. Bacteriol. 178 1996 840-845
    • (1996) J. Bacteriol. , vol.178 , pp. 840-845
    • Yang, C.1    Kim, J.2    Molinari, E.3    Dassarma, S.4
  • 36
    • 0001818891 scopus 로고
    • Measuring correlations in symbol sequences
    • H. Herzel, and I. Grosse Measuring correlations in symbol sequences Physica A 216 1995 518 542
    • (1995) Physica a , vol.216 , pp. 518-542
    • Herzel, H.1    Grosse, I.2
  • 38
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • D. Goodsell, and R. Dickerson Bending and curvature calculations in B-DNA Nucl. Acids Res. 22 1994 5497 5503
    • (1994) Nucl. Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.1    Dickerson, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.