-
1
-
-
0035182436
-
Nucleosome formation potential of eukaryotic DNA: Calculation and promoters analysis
-
Levitsky,V.G., Podkolodnaya,O.A., Kolchanov,N.A. and Podkolodny,N.L. (2001) Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics, 17, 998-1010.
-
(2001)
Bioinformatics
, vol.17
, pp. 998-1010
-
-
Levitsky, V.G.1
Podkolodnaya, O.A.2
Kolchanov, N.A.3
Podkolodny, N.L.4
-
2
-
-
33749583306
-
-
3rd edn., McGraw-Hill, Boston. Ch. 12
-
Weaver,R.F. (2005) Molecular Biology, 3rd edn., McGraw-Hill, Boston. Ch. 12, 13, pp. 342-423.
-
(2005)
Molecular Biology
, vol.13
, pp. 342-423
-
-
Weaver, R.F.1
-
3
-
-
0032403947
-
Specific local histone-DNA sequence contacts facilitate high-affinity, non-cooperative nucleosome binding of both adf-1 and GAGA factor
-
Gao,J. and Benyajati,C. (1998) Specific local histone-DNA sequence contacts facilitate high-affinity, non-cooperative nucleosome binding of both adf-1 and GAGA factor. Nucleic Acids Res., 26, 5394-5401.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 5394-5401
-
-
Gao, J.1
Benyajati, C.2
-
4
-
-
8644230848
-
DNA instructed displacement of histones H2A and H2B at an inducible promoter
-
Vicent,G.P., Nacht,A.S., Smith,C.L., Peterson,C.L., Dimitrov,S. and Beato,M. (2004) DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol. Cell, 16, 439-452.
-
(2004)
Mol. Cell
, vol.16
, pp. 439-452
-
-
Vicent, G.P.1
Nacht, A.S.2
Smith, C.L.3
Peterson, C.L.4
Dimitrov, S.5
Beato, M.6
-
5
-
-
0036200587
-
Liver-enriched transcription factors in liver function and development. Part I: The hepatocyte nuclear factor network and liver-specific gene expression
-
Schrem,H., Klempnauer,J. and Borlak,J. (2002) Liver-enriched transcription factors in liver function and development. Part I: the hepatocyte nuclear factor network and liver-specific gene expression. Pharmacol. Rev., 54, 129-158.
-
(2002)
Pharmacol. Rev.
, vol.54
, pp. 129-158
-
-
Schrem, H.1
Klempnauer, J.2
Borlak, J.3
-
6
-
-
0042733700
-
Getting into chromatin: How do transcription factors get past the histones?
-
Morse,R.H. (2003) Getting into chromatin: how do transcription factors get past the histones? Biochem. Cell. Biol., 81, 101-112.
-
(2003)
Biochem. Cell. Biol.
, vol.81
, pp. 101-112
-
-
Morse, R.H.1
-
7
-
-
31544446038
-
Transcriptional activators are dispensable for transcription in the absence of spt6-mediated chromatin reassembly of promoter regions
-
Adkins,M.W. and Tyler,J.K. (2006) Transcriptional activators are dispensable for transcription in the absence of spt6-mediated chromatin reassembly of promoter regions. Mol. Cell, 21, 405-416.
-
(2006)
Mol. Cell
, vol.21
, pp. 405-416
-
-
Adkins, M.W.1
Tyler, J.K.2
-
8
-
-
14544303760
-
Structure and dynamic properties of nucleosome core particles
-
Chakravarthy,S., Park,Y.J., Chodaparambil,J., Edayathumangalam,R.S. and Luger,K. (2005) Structure and dynamic properties of nucleosome core particles. FEBS Lett., 579, 895-898.
-
(2005)
FEBS Lett.
, vol.579
, pp. 895-898
-
-
Chakravarthy, S.1
Park, Y.J.2
Chodaparambil, J.3
Edayathumangalam, R.S.4
Luger, K.5
-
9
-
-
1842411320
-
X-ray structure of the nucleosome core particle at 2.8 Å resolution
-
Luger,K., Mader,A.W., Richmond,R.K., Sargent,D.F. and Richmond,T.J. (1997) X-ray structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260.
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mader, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
10
-
-
0036307707
-
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
-
Davey,C.A., Sargent,D.F., Luger,K., Maeder,A.W. and Richmond,T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol., 319, 1097-1113.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1097-1113
-
-
Davey, C.A.1
Sargent, D.F.2
Luger, K.3
Maeder, A.W.4
Richmond, T.J.5
-
11
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond,T.J. and Davey,C.A. (2003) The structure of DNA in the nucleosome core. Nature, 423, 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
12
-
-
1542768922
-
New approaches to DNA in the crystal and in solution
-
In Cozzarelli,N.R. and Wang,J.C. (eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Monograph 20
-
Drew,H.R., McCall,M.J. and Calladine,C.R. (1990) New approaches to DNA in the crystal and in solution. In Cozzarelli,N.R. and Wang,J.C. (eds), DNA Topology and its Biological Effects. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Monograph 20, pp. 1-56.
-
(1990)
DNA Topology and Its Biological Effects
, pp. 1-56
-
-
Drew, H.R.1
McCall, M.J.2
Calladine, C.R.3
-
13
-
-
0002524447
-
Bending of DNA in nucleoprotein complexes
-
In Cozzarelli,N.R. and Wang,J.C. (eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Monograph 20
-
Travers,A.A. and Klug,A. (1990) Bending of DNA in nucleoprotein complexes. In Cozzarelli,N.R. and Wang,J.C. (eds), DNA Topology and its Biological Effects. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Monograph 20, pp. 57-106.
-
(1990)
DNA Topology and Its Biological Effects
, pp. 57-106
-
-
Travers, A.A.1
Klug, A.2
-
14
-
-
0029664913
-
The [(G/C)3NN]n motif: A common DNA repeat that excludes nucleosomes
-
Wang,Y.H. and Griffith,J.D. (1996) The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes. Proc. Natl Acad. Sci. USA, 93, 8863-8867.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 8863-8867
-
-
Wang, Y.H.1
Griffith, J.D.2
-
15
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell,S.C., Drew,H.R. and Travers,A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
-
(1986)
J. Mol. Biol.
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
16
-
-
0034310723
-
Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo
-
Suter,B., Schnappauf,G. and Thoma,F. (2000) Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res., 28, 4083-4089.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4083-4089
-
-
Suter, B.1
Schnappauf, G.2
Thoma, F.3
-
17
-
-
0035900536
-
Molecular dynamics simulations of B′-DNA: Sequence effects on A-tract-induced bending and flexibility
-
McConnell,K.J. and Beveridge,D.L. (2001) Molecular dynamics simulations of B′-DNA: sequence effects on A-tract-induced bending and flexibility. J. Mol. Biol., 314, 23-40.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 23-40
-
-
McConnell, K.J.1
Beveridge, D.L.2
-
18
-
-
13444252849
-
NPRD: Nucleosome Positioning Region Database
-
Levitsky,V.G., Katokhin,A.V., Podkolodnaya,O.A., Furman,D.P. and Kolchanov,N.A. (2005) NPRD: Nucleosome Positioning Region Database. Nucleic Acids Res., 33, D67-D70.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Levitsky, V.G.1
Katokhin, A.V.2
Podkolodnaya, O.A.3
Furman, D.P.4
Kolchanov, N.A.5
-
19
-
-
0020042771
-
Mapping the in vivo arrangement of nucleosomes on simian virus 40 chromatin by the photoaddition of radioactive hydroxymethyltrimethylpsoralen
-
Robinson,G.W. and Hallick,L.M. (1982) Mapping the in vivo arrangement of nucleosomes on simian virus 40 chromatin by the photoaddition of radioactive hydroxymethyltrimethylpsoralen. J. Virol., 41, 78-87.
-
(1982)
J. Virol.
, vol.41
, pp. 78-87
-
-
Robinson, G.W.1
Hallick, L.M.2
-
20
-
-
0021699563
-
A direct analysis of transcribed minichromosomes: All transcribed SV40 minichromosomes have a nuclease-hypersensitive region within a nucleosome-free domain
-
Choder,M., Bratosin,S. and Aloni,Y. (1984) A direct analysis of transcribed minichromosomes: all transcribed SV40 minichromosomes have a nuclease-hypersensitive region within a nucleosome-free domain. EMBO J., 3, 2929-2936.
-
(1984)
EMBO J.
, vol.3
, pp. 2929-2936
-
-
Choder, M.1
Bratosin, S.2
Aloni, Y.3
-
21
-
-
0027180164
-
Association of nucleosome-free regions and basal transcription factors with in vivo-assembled chromatin templates active in vitro
-
Batson,S.C., Rimsky,S., Sundseth,R. and Hansen,U. (1993) Association of nucleosome-free regions and basal transcription factors with in vivo-assembled chromatin templates active in vitro. Nucleic Acids Res., 21, 3459-3468.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 3459-3468
-
-
Batson, S.C.1
Rimsky, S.2
Sundseth, R.3
Hansen, U.4
-
22
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su,A.I., Wiltshire,T., Batalov,S., Lapp,H., Ching,K.A., Block,D., Zhang,J., Soden,R., Hayakawa,M., Kreiman,G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
-
23
-
-
0347756647
-
DBTSS, DataBase of Transcriptional Start Sites: Progress report 2004
-
Suzuki,Y., Yamashita,R., Sugano,S. and Nakai,K. (2004) DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res., 32, D78-D81.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Suzuki, Y.1
Yamashita, R.2
Sugano, S.3
Nakai, K.4
-
24
-
-
3242879056
-
Nucleosomal DNA organization: An integrated information system
-
In Kolchanov,N. and Hofestaedt,R. (eds), Kluwer Academic Publishers, Boston
-
Levitsky,V.G., Katokhin,A.V., Podkolodnaya,O.A. and Furman,D.P. (2004) Nucleosomal DNA organization: an integrated information system. In Kolchanov,N. and Hofestaedt,R. (eds), Bioinformatics of Genome Regulation and Structure. Kluwer Academic Publishers, Boston, pp. 3-12.
-
(2004)
Bioinformatics of Genome Regulation and Structure
, pp. 3-12
-
-
Levitsky, V.G.1
Katokhin, A.V.2
Podkolodnaya, O.A.3
Furman, D.P.4
-
25
-
-
0030249381
-
The role of general initiation factors in transcription by RNA polymerase II
-
Roeder,R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci., 21, 327-335.
-
(1996)
Trends Biochem. Sci.
, vol.21
, pp. 327-335
-
-
Roeder, R.G.1
-
26
-
-
0037154984
-
The RNA polymerase II machinery: Structure illuminates function
-
Woychik,N.A. and Hampsey,M. (2002) The RNA polymerase II machinery: structure illuminates function. Cell, 108, 453-463.
-
(2002)
Cell
, vol.108
, pp. 453-463
-
-
Woychik, N.A.1
Hampsey, M.2
-
27
-
-
0034991911
-
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
-
Suzuki,Y., Taira,H., Tsunoda,T., Mizushima-Sugano,J., Sese,J., Hata,H., Ota,T., Isogai,T., Tanaka,T., Morishita,S. et al. (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep., 2, 388-393.
-
(2001)
EMBO Rep.
, vol.2
, pp. 388-393
-
-
Suzuki, Y.1
Taira, H.2
Tsunoda, T.3
Mizushima-Sugano, J.4
Sese, J.5
Hata, H.6
Ota, T.7
Isogai, T.8
Tanaka, T.9
Morishita, S.10
-
28
-
-
13744263543
-
Noncoding DNA, isochores and gene expression: Nucleosome formation potential
-
Vinogradov,A.E. (2005) Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res., 33, 559-563.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 559-563
-
-
Vinogradov, A.E.1
-
29
-
-
25444499171
-
Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes
-
Ganapathi,M., Srivastava,P., Kumar,S., Sutar,S.K.D., Kumar,K., Dasgupta,D., Singh,G.P., Brahmachari,V. and Brahmachari,S.K. (2005) Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics, 6, 126.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 126
-
-
Ganapathi, M.1
Srivastava, P.2
Kumar, S.3
Sutar, S.K.D.4
Kumar, K.5
Dasgupta, D.6
Singh, G.P.7
Brahmachari, V.8
Brahmachari, S.K.9
-
30
-
-
0032516764
-
TGGA repeats impair nucleosome formation
-
Cao,H., Widlund,H.R., Simonsson,T. and Kubista,M. (1998) TGGA repeats impair nucleosome formation. J. Mol. Biol., 281, 253-260.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 253-260
-
-
Cao, H.1
Widlund, H.R.2
Simonsson, T.3
Kubista, M.4
-
31
-
-
0037133565
-
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
-
Takai,D. and Jones,P.A. (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl Acad. Sci. USA, 99, 3740-3745.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 3740-3745
-
-
Takai, D.1
Jones, P.A.2
-
32
-
-
0042329754
-
Structure, function and evolution of CpG island promoters
-
Antequera,F. (2003) Structure, function and evolution of CpG island promoters. Cell. Mol. Life Sci., 60, 1647-1658.
-
(2003)
Cell. Mol. Life Sci.
, vol.60
, pp. 1647-1658
-
-
Antequera, F.1
-
33
-
-
0034775396
-
Nucleosomes are translationally positioned on the active allele and rotationally positioned on the inactive allele of the HPRT promoter
-
Chen,C. and Yang,T.P. (2001) Nucleosomes are translationally positioned on the active allele and rotationally positioned on the inactive allele of the HPRT promoter. Mol. Cell. Biol., 21, 7682-7695.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 7682-7695
-
-
Chen, C.1
Yang, T.P.2
-
34
-
-
0141753136
-
Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences
-
Baumann,M., Mamais,A., McBlane,F., Xiao,H. and Boyes,J. (2003) Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences. EMBO J., 22, 5197-5207.
-
(2003)
EMBO J.
, vol.22
, pp. 5197-5207
-
-
Baumann, M.1
Mamais, A.2
McBlane, F.3
Xiao, H.4
Boyes, J.5
-
35
-
-
0037414332
-
Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter
-
Powell,N.G., Ferreiro,J., Karabetsou,N., Mellor,J. and Waters,R. (2003) Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter. DNA Repair, 2, 375-386.
-
(2003)
DNA Repair
, vol.2
, pp. 375-386
-
-
Powell, N.G.1
Ferreiro, J.2
Karabetsou, N.3
Mellor, J.4
Waters, R.5
-
36
-
-
0037474533
-
Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions
-
Davey,C., Fraser,R., Smolle,M., Simmen,M.W. and Allan,J. (2003) Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions. J. Mol. Biol., 325, 873-887.
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 873-887
-
-
Davey, C.1
Fraser, R.2
Smolle, M.3
Simmen, M.W.4
Allan, J.5
-
37
-
-
20444429051
-
Gene splice sites correlate with nucleosome positions
-
Kogan,S. and Trifonov,E.N. (2005) Gene splice sites correlate with nucleosome positions. Gene, 352, 57-62.
-
(2005)
Gene
, vol.352
, pp. 57-62
-
-
Kogan, S.1
Trifonov, E.N.2
-
38
-
-
16344367080
-
DNA methylation, nucleosome formation and positioning
-
Pennings,S., Allan,J. and Davey,C.S. (2005) DNA methylation, nucleosome formation and positioning. Brief Funct. Genomic Proteomic., 3, 351-361.
-
(2005)
Brief Funct. Genomic Proteomic.
, vol.3
, pp. 351-361
-
-
Pennings, S.1
Allan, J.2
Davey, C.S.3
|