-
1
-
-
1642473149
-
DNase i behaves as a transcription factor which modulates Fas expression in human cells
-
Oliveri M, et al. (2004) DNase I behaves as a transcription factor which modulates Fas expression in human cells. Eur J Immunol 34(1):273-279.
-
(2004)
Eur J Immunol
, vol.34
, Issue.1
, pp. 273-279
-
-
Oliveri, M.1
-
2
-
-
0023818825
-
Structure refined to 2A of a nicked DNA octanu-cleotide complex with DNase i
-
Suck D, Lahm A, Oefner C (1988) Structure refined to 2A of a nicked DNA octanu-cleotide complex with DNase I. Nature 332(6163):464-468.
-
(1988)
Nature
, vol.332
, Issue.6163
, pp. 464-468
-
-
Suck, D.1
Lahm, A.2
Oefner, C.3
-
3
-
-
0026447731
-
X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution
-
Weston SA, Lahm A, Suck D (1992) X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J Mol Biol 226(4):1237-1256.
-
(1992)
J Mol Biol
, vol.226
, Issue.4
, pp. 1237-1256
-
-
Weston, S.A.1
Lahm, A.2
Suck, D.3
-
4
-
-
0024310233
-
DNA flexibility variation may dominate DNase i cleavage
-
Hogan ME, Roberson MW, Austin RH (1989) DNA flexibility variation may dominate DNase I cleavage. Proc Natl Acad Sci USA 86(23):9273-9277.
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, Issue.23
, pp. 9273-9277
-
-
Hogan, M.E.1
Roberson, M.W.2
Austin, R.H.3
-
5
-
-
70450222293
-
Sequence-dependent DNA flexibility mediates DNase i cleavage
-
Heddi B, Abi-Ghanem J, Lavigne M, Hartmann B (2010) Sequence-dependent DNA flexibility mediates DNase I cleavage. J Mol Biol 395(1):123-133.
-
(2010)
J Mol Biol
, vol.395
, Issue.1
, pp. 123-133
-
-
Heddi, B.1
Abi-Ghanem, J.2
Lavigne, M.3
Hartmann, B.4
-
6
-
-
20844435623
-
High-throughput localization of functional elements by quantitative chromatin profiling
-
Dorschner MO, et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods 1(3):219-225.
-
(2004)
Nat Methods
, vol.1
, Issue.3
, pp. 219-225
-
-
Dorschner, M.O.1
-
7
-
-
10044264270
-
Discovery of functional noncoding elements by digital analysis of chromatin structure
-
Sabo PJ, et al. (2004) Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci USA 101(48):16837-16842.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.48
, pp. 16837-16842
-
-
Sabo, P.J.1
-
8
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
John S, et al. (2011) Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43(3):264-268.
-
(2011)
Nat Genet
, vol.43
, Issue.3
, pp. 264-268
-
-
John, S.1
-
9
-
-
33745416080
-
Genome-scale mapping of DNase i sensitivity in vivo using tiling DNA microarrays
-
Sabo PJ, et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3(7):511-518.
-
(2006)
Nat Methods
, vol.3
, Issue.7
, pp. 511-518
-
-
Sabo, P.J.1
-
10
-
-
0018199224
-
DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
-
Galas DJ, Schmitz A (1978) DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5(9):3157-3170.
-
(1978)
Nucleic Acids Res
, vol.5
, Issue.9
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
11
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth JR, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283-289.
-
(2009)
Nat Methods
, vol.6
, Issue.4
, pp. 283-289
-
-
Hesselberth, J.R.1
-
12
-
-
16344367080
-
DNA methylation, nucleosome formation and positioning
-
Pennings S, Allan J, Davey CS (2005) DNA methylation, nucleosome formation and positioning. Brief Funct Genomics Proteomics 3(4):351-361.
-
(2005)
Brief Funct Genomics Proteomics
, vol.3
, Issue.4
, pp. 351-361
-
-
Pennings, S.1
Allan, J.2
Davey, C.S.3
-
13
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
Suzuki MM, Bird A (2008) DNA methylation landscapes: Provocative insights from epigenomics. Nat Rev Genet 9(6):465-476.
-
(2008)
Nat Rev Genet
, vol.9
, Issue.6
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
14
-
-
40449104358
-
Transient cyclical methylation of promoter DNA
-
Kangaspeska S, et al. (2008) Transient cyclical methylation of promoter DNA. Nature 452(7183):112-115.
-
(2008)
Nature
, vol.452
, Issue.7183
, pp. 112-115
-
-
Kangaspeska, S.1
-
15
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1): 6-21.
-
(2002)
Genes Dev
, vol.16
, Issue.1
, pp. 6-21
-
-
Bird, A.1
-
16
-
-
33751505540
-
DNA methylation profiling of human chromosomes 6, 20 and 22
-
Eckhardt F, et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38(12):1378-1385.
-
(2006)
Nat Genet
, vol.38
, Issue.12
, pp. 1378-1385
-
-
Eckhardt, F.1
-
17
-
-
34047116826
-
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
-
Weber M, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39(4):457-466.
-
(2007)
Nat Genet
, vol.39
, Issue.4
, pp. 457-466
-
-
Weber, M.1
-
18
-
-
40549111302
-
All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues
-
Rozenberg JM, et al. (2008) All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics 9:67.
-
(2008)
BMC Genomics
, vol.9
, pp. 67
-
-
Rozenberg, J.M.1
-
19
-
-
78650584064
-
CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes
-
Rishi V, et al. (2010) CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. Proc Natl Acad Sci USA 107(47): 20311-20316.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.47
, pp. 20311-20316
-
-
Rishi, V.1
-
20
-
-
64649095501
-
Nuance in the double-helix and its role in protein-DNA recognition
-
Rohs R, West SM, Liu P, Honig B (2009) Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol 19(2):171-177.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.2
, pp. 171-177
-
-
Rohs, R.1
West, S.M.2
Liu, P.3
Honig, B.4
-
21
-
-
35548931586
-
Functional specificity of a Hox protein mediated by the recognition of minor groove structure
-
Joshi R, et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131(3):530-543.
-
(2007)
Cell
, vol.131
, Issue.3
, pp. 530-543
-
-
Joshi, R.1
-
22
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
Rohs R, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461(7268):1248-1253.
-
(2009)
Nature
, vol.461
, Issue.7268
, pp. 1248-1253
-
-
Rohs, R.1
-
23
-
-
77950519937
-
Origins of specificity in protein-DNA recognition
-
Rohs R, et al. (2010) Origins of specificity in protein-DNA recognition. Annu Rev Bi-ochem 79:233-269.
-
(2010)
Annu Rev Bi-ochem
, vol.79
, pp. 233-269
-
-
Rohs, R.1
-
24
-
-
83255188878
-
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
-
Slattery M, et al. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147(6):1270-1282.
-
(2011)
Cell
, vol.147
, Issue.6
, pp. 1270-1282
-
-
Slattery, M.1
-
25
-
-
77950484709
-
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs
-
Kitayner M, et al. (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol 17(4):423-429.
-
(2010)
Nat Struct Mol Biol
, vol.17
, Issue.4
, pp. 423-429
-
-
Kitayner, M.1
-
26
-
-
0028446567
-
DNA recognition by DNase i
-
Suck D (1994) DNA recognition by DNase I. J Mol Recognit 7(2):65-70.
-
(1994)
J Mol Recognit
, vol.7
, Issue.2
, pp. 65-70
-
-
Suck, D.1
-
27
-
-
0021140818
-
DNA structural variations in the E. coli tyrT promoter
-
Drew HR, Travers AA (1984) DNA structural variations in the E. coli tyrT promoter. Cell 37(2):491-502.
-
(1984)
Cell
, vol.37
, Issue.2
, pp. 491-502
-
-
Drew, H.R.1
Travers, A.A.2
-
28
-
-
0028220190
-
Characterization of preferred deoxyribonuclease i cleavage sites
-
Herrera JE, Chaires JB (1994) Characterization of preferred deoxyribonuclease I cleavage sites. J Mol Biol 236(2):405-411.
-
(1994)
J Mol Biol
, vol.236
, Issue.2
, pp. 405-411
-
-
Herrera, J.E.1
Chaires, J.B.2
-
29
-
-
0029039118
-
Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides
-
Brukner I, Sánchez R, Suck D, Pongor S (1995) Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides. EMBO J 14(8):1812-1818.
-
(1995)
EMBO J
, vol.14
, Issue.8
, pp. 1812-1818
-
-
Brukner, I.1
Sánchez, R.2
Suck, D.3
Pongor, S.4
-
30
-
-
0033231468
-
Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation
-
Marcourt L, Cordier C, Couesnon T, Dodin G (1999) Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation. Euro J Biochem 265(3):1032-1042.
-
(1999)
Euro J Biochem
, vol.265
, Issue.3
, pp. 1032-1042
-
-
Marcourt, L.1
Cordier, C.2
Couesnon, T.3
Dodin, G.4
-
31
-
-
0026354983
-
DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex
-
Lahm A, Suck D (1991) DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. J Mol Biol 222(3):645-667.
-
(1991)
J Mol Biol
, vol.222
, Issue.3
, pp. 645-667
-
-
Lahm, A.1
Suck, D.2
-
32
-
-
0019387685
-
Sequence-dependent variation in the conformation of DNA
-
Lomonossoff GP, Butler PJ, Klug A (1981) Sequence-dependent variation in the conformation of DNA. J Mol Biol 149(4):745-760.
-
(1981)
J Mol Biol
, vol.149
, Issue.4
, pp. 745-760
-
-
Lomonossoff, G.P.1
Butler, P.J.2
Klug, A.3
-
33
-
-
0025342685
-
Sequence-dependent structural variations of DNA revealed by DNase i
-
Brukner I, Jurukovski V, Savic A (1990) Sequence-dependent structural variations of DNA revealed by DNase I. Nucleic Acids Res 18(4):891-894.
-
(1990)
Nucleic Acids Res
, vol.18
, Issue.4
, pp. 891-894
-
-
Brukner, I.1
Jurukovski, V.2
Savic, A.3
-
34
-
-
84858708697
-
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA
-
Bishop EP, et al. (2011) A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol 6(12):1314-1320.
-
(2011)
ACS Chem Biol
, vol.6
, Issue.12
, pp. 1314-1320
-
-
Bishop, E.P.1
-
35
-
-
0025017245
-
DNA methylation. The effect of minor bases on DNA-protein interactions
-
Adams RL (1990) DNA methylation. The effect of minor bases on DNA-protein interactions. Biochem J 265(2):309-320.
-
(1990)
Biochem J
, vol.265
, Issue.2
, pp. 309-320
-
-
Adams, R.L.1
-
36
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315-322.
-
(2009)
Nature
, vol.462
, Issue.7271
, pp. 315-322
-
-
Lister, R.1
-
37
-
-
0022525152
-
The effect of HhaI methylation on DNA local structure
-
Fox KR (1986) The effect of HhaI methylation on DNA local structure. Biochem J 234(1):213-216.
-
(1986)
Biochem J
, vol.234
, Issue.1
, pp. 213-216
-
-
Fox, K.R.1
-
38
-
-
0027723229
-
Differences in the accessibility of methylated and unmethylated DNA to DNase i
-
Kochanek S, Renz D, Doerfler W (1993) Differences in the accessibility of methylated and unmethylated DNA to DNase I. Nucleic Acids Res 21(25):5843-5845.
-
(1993)
Nucleic Acids Res
, vol.21
, Issue.25
, pp. 5843-5845
-
-
Kochanek, S.1
Renz, D.2
Doerfler, W.3
-
40
-
-
65249167505
-
DNA binding site sequence directs glucocorticoid receptor structure and activity
-
Meijsing SH, et al. (2009) DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324(5925):407-410.
-
(2009)
Science
, vol.324
, Issue.5925
, pp. 407-410
-
-
Meijsing, S.H.1
-
41
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
Neph S, et al. (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489(7414):83-90.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 83-90
-
-
Neph, S.1
-
42
-
-
44449117557
-
Using RNase sequence specificity to refine the identification of RNA-protein binding regions
-
Wang X, et al. (2008) Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics 9(Suppl 1):S17.
-
(2008)
BMC Genomics
, vol.9-17
, Issue.SUPPL. 1
-
-
Wang, X.1
-
43
-
-
79952264847
-
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
-
Lister R, et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336):68-73.
-
(2011)
Nature
, vol.471
, Issue.7336
, pp. 68-73
-
-
Lister, R.1
-
44
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
Hansen KD, et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43(8):768-775.
-
(2011)
Nat Genet
, vol.43
, Issue.8
, pp. 768-775
-
-
Hansen, K.D.1
-
45
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu RK, et al. (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466(7304):388-392.
-
(2010)
Nature
, vol.466
, Issue.7304
, pp. 388-392
-
-
Chodavarapu, R.K.1
-
46
-
-
84870552401
-
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
-
Kelly TK, et al. (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22(12):2497-2506.
-
(2012)
Genome Res
, vol.22
, Issue.12
, pp. 2497-2506
-
-
Kelly, T.K.1
-
47
-
-
77953311493
-
Electrostatic interactions between argi-nines and the minor groove in the nucleosome
-
West SM, Rohs R, Mann RS, Honig B (2010) Electrostatic interactions between argi-nines and the minor groove in the nucleosome. J Biomol Struct Dyn 27(6):861-866.
-
(2010)
J Biomol Struct Dyn
, vol.27
, Issue.6
, pp. 861-866
-
-
West, S.M.1
Rohs, R.2
Mann, R.S.3
Honig, B.4
|