-
1
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
FANTOM Consortium
-
R. Andersson, C. Gebhard, I. Miguel-Escalada, I. Hoof, J. Bornholdt, M. Boyd, Y. Chen, X. Zhao, C. Schmidl, T. Suzuki FANTOM Consortium An atlas of active enhancers across human cell types and tissues Nature 507 2014 455 461
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
Chen, Y.7
Zhao, X.8
Schmidl, C.9
Suzuki, T.10
-
2
-
-
83255192190
-
Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells
-
C. Andreu-Vieyra, J. Lai, B.P. Berman, B. Frenkel, L. Jia, P.A. Jones, and G.A. Coetzee Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells Mol. Cell. Biol. 31 2011 4648 4662
-
(2011)
Mol. Cell. Biol.
, vol.31
, pp. 4648-4662
-
-
Andreu-Vieyra, C.1
Lai, J.2
Berman, B.P.3
Frenkel, B.4
Jia, L.5
Jones, P.A.6
Coetzee, G.A.7
-
3
-
-
0033561173
-
Roles for Nkx3.1 in prostate development and cancer
-
R. Bhatia-Gaur, A.A. Donjacour, P.J. Sciavolino, M. Kim, N. Desai, P. Young, C.R. Norton, T. Gridley, R.D. Cardiff, and G.R. Cunha Roles for Nkx3.1 in prostate development and cancer Genes Dev. 13 1999 966 977
-
(1999)
Genes Dev.
, vol.13
, pp. 966-977
-
-
Bhatia-Gaur, R.1
Donjacour, A.A.2
Sciavolino, P.J.3
Kim, M.4
Desai, N.5
Young, P.6
Norton, C.R.7
Gridley, T.8
Cardiff, R.D.9
Cunha, G.R.10
-
4
-
-
33846682284
-
NKX3.1 homeodomain protein binds to topoisomerase i and enhances its activity
-
C. Bowen, A. Stuart, J.H. Ju, J. Tuan, J. Blonder, T.P. Conrads, T.D. Veenstra, and E.P. Gelmann NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity Cancer Res. 67 2007 455 464
-
(2007)
Cancer Res.
, vol.67
, pp. 455-464
-
-
Bowen, C.1
Stuart, A.2
Ju, J.H.3
Tuan, J.4
Blonder, J.5
Conrads, T.P.6
Veenstra, T.D.7
Gelmann, E.P.8
-
5
-
-
0034923502
-
DNA topoisomerases: Structure, function, and mechanism
-
J.J. Champoux DNA topoisomerases: structure, function, and mechanism Annu. Rev. Biochem. 70 2001 369 413
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 369-413
-
-
Champoux, J.J.1
-
6
-
-
84899688897
-
Deletion of individual Ku subunits in mice causes an NHEJ-independent phenotype potentially by altering apurinic/apyrimidinic site repair
-
Y.J. Choi, H. Li, M.Y. Son, X.H. Wang, J.L. Fornsaglio, R.W. Sobol, M. Lee, J. Vijg, S. Imholz, and M.E. Dollé Deletion of individual Ku subunits in mice causes an NHEJ-independent phenotype potentially by altering apurinic/apyrimidinic site repair PLoS ONE 9 2014 e86358
-
(2014)
PLoS ONE
, vol.9
, pp. e86358
-
-
Choi, Y.J.1
Li, H.2
Son, M.Y.3
Wang, X.H.4
Fornsaglio, J.L.5
Sobol, R.W.6
Lee, M.7
Vijg, J.8
Imholz, S.9
Dollé, M.E.10
-
7
-
-
84888343067
-
Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element
-
L. Clinckemalie, L. Spans, V. Dubois, M. Laurent, C. Helsen, S. Joniau, and F. Claessens Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element Mol. Endocrinol. 27 2013 2028 2040
-
(2013)
Mol. Endocrinol.
, vol.27
, pp. 2028-2040
-
-
Clinckemalie, L.1
Spans, L.2
Dubois, V.3
Laurent, M.4
Helsen, C.5
Joniau, S.6
Claessens, F.7
-
8
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
9
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
X. Darzacq, Y. Shav-Tal, V. de Turris, Y. Brody, S.M. Shenoy, R.D. Phair, and R.H. Singer In vivo dynamics of RNA polymerase II transcription Nat. Struct. Mol. Biol. 14 2007 796 806
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
De Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
10
-
-
84896267457
-
Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair
-
L. Davis, and N. Maizels Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair Proc. Natl. Acad. Sci. USA 111 2014 E924 E932
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. E924-E932
-
-
Davis, L.1
Maizels, N.2
-
11
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
F. De Santa, I. Barozzi, F. Mietton, S. Ghisletti, S. Polletti, B.K. Tusi, H. Muller, J. Ragoussis, C.-L. Wei, and G. Natoli A large fraction of extragenic RNA pol II transcription sites overlap enhancers PLoS Biol. 8 2010 e1000384
-
(2010)
PLoS Biol.
, vol.8
, pp. e1000384
-
-
De Santa, F.1
Barozzi, I.2
Mietton, F.3
Ghisletti, S.4
Polletti, S.5
Tusi, B.K.6
Muller, H.7
Ragoussis, J.8
Wei, C.-L.9
Natoli, G.10
-
12
-
-
80052008241
-
Linking RNA polymerase backtracking to genome instability in E. Coli
-
D. Dutta, K. Shatalin, V. Epshtein, M.E. Gottesman, and E. Nudler Linking RNA polymerase backtracking to genome instability in E. coli Cell 146 2011 533 543
-
(2011)
Cell
, vol.146
, pp. 533-543
-
-
Dutta, D.1
Shatalin, K.2
Epshtein, V.3
Gottesman, M.E.4
Nudler, E.5
-
13
-
-
77954841539
-
Loss of Topoisomerase i leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis
-
A. El Hage, S.L. French, A.L. Beyer, and D. Tollervey Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis Genes Dev. 24 2010 1546 1558
-
(2010)
Genes Dev.
, vol.24
, pp. 1546-1558
-
-
El Hage, A.1
French, S.L.2
Beyer, A.L.3
Tollervey, D.4
-
14
-
-
80053538947
-
A DNA repair complex functions as an Oct4/Sox2 coactivator in embryonic stem cells
-
Y.W. Fong, C. Inouye, T. Yamaguchi, C. Cattoglio, I. Grubisic, and R. Tjian A DNA repair complex functions as an Oct4/Sox2 coactivator in embryonic stem cells Cell 147 2011 120 131
-
(2011)
Cell
, vol.147
, pp. 120-131
-
-
Fong, Y.W.1
Inouye, C.2
Yamaguchi, T.3
Cattoglio, C.4
Grubisic, I.5
Tjian, R.6
-
15
-
-
84887151305
-
The intertwined roles of transcription and repair proteins
-
Y.W. Fong, C. Cattoglio, and R. Tjian The intertwined roles of transcription and repair proteins Mol. Cell 52 2013 291 302
-
(2013)
Mol. Cell
, vol.52
, pp. 291-302
-
-
Fong, Y.W.1
Cattoglio, C.2
Tjian, R.3
-
16
-
-
33846690407
-
Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors
-
I. Garcia-Bassets, Y.S. Kwon, F. Telese, G.G. Prefontaine, K.R. Hutt, C.S. Cheng, B.G. Ju, K.A. Ohgi, J. Wang, and L. Escoubet-Lozach Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors Cell 128 2007 505 518
-
(2007)
Cell
, vol.128
, pp. 505-518
-
-
Garcia-Bassets, I.1
Kwon, Y.S.2
Telese, F.3
Prefontaine, G.G.4
Hutt, K.R.5
Cheng, C.S.6
Ju, B.G.7
Ohgi, K.A.8
Wang, J.9
Escoubet-Lozach, L.10
-
17
-
-
0026648674
-
Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation
-
Y. Gavrieli, Y. Sherman, and S.A. Ben-Sasson Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation J. Cell Biol. 119 1992 493 501
-
(1992)
J. Cell Biol.
, vol.119
, pp. 493-501
-
-
Gavrieli, Y.1
Sherman, Y.2
Ben-Sasson, S.A.3
-
18
-
-
33847193121
-
XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps
-
J. Gu, H. Lu, B. Tippin, N. Shimazaki, M.F. Goodman, and M.R. Lieber XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps EMBO J. 26 2007 1010 1023
-
(2007)
EMBO J.
, vol.26
, pp. 1010-1023
-
-
Gu, J.1
Lu, H.2
Tippin, B.3
Shimazaki, N.4
Goodman, M.F.5
Lieber, M.R.6
-
19
-
-
77955171924
-
NKX3.1 as a marker of prostatic origin in metastatic tumors
-
B. Gurel, T.Z. Ali, E.A. Montgomery, S. Begum, J. Hicks, M. Goggins, C.G. Eberhart, D.P. Clark, C.J. Bieberich, J.I. Epstein, and A.M. De Marzo NKX3.1 as a marker of prostatic origin in metastatic tumors Am. J. Surg. Pathol. 34 2010 1097 1105
-
(2010)
Am. J. Surg. Pathol.
, vol.34
, pp. 1097-1105
-
-
Gurel, B.1
Ali, T.Z.2
Montgomery, E.A.3
Begum, S.4
Hicks, J.5
Goggins, M.6
Eberhart, C.G.7
Clark, D.P.8
Bieberich, C.J.9
Epstein, J.I.10
De Marzo, A.M.11
-
20
-
-
84881171344
-
Enhancer transcripts mark active estrogen receptor binding sites
-
N. Hah, S. Murakami, A. Nagari, C.G. Danko, and W.L. Kraus Enhancer transcripts mark active estrogen receptor binding sites Genome Res. 23 2013 1210 1223
-
(2013)
Genome Res.
, vol.23
, pp. 1210-1223
-
-
Hah, N.1
Murakami, S.2
Nagari, A.3
Danko, C.G.4
Kraus, W.L.5
-
21
-
-
78149442129
-
MRE11 function in response to topoisomerase poisons is independent of its function in double-strand break repair in Saccharomyces cerevisiae
-
N.K. Hamilton, and N. Maizels MRE11 function in response to topoisomerase poisons is independent of its function in double-strand break repair in Saccharomyces cerevisiae PLoS ONE 5 2010 e15387
-
(2010)
PLoS ONE
, vol.5
, pp. e15387
-
-
Hamilton, N.K.1
Maizels, N.2
-
22
-
-
0026752261
-
A transcriptional enhancer whose function imposes a requirement that proteins track along DNA
-
D.R. Herendeen, G.A. Kassavetis, and E.P. Geiduschek A transcriptional enhancer whose function imposes a requirement that proteins track along DNA Science 256 1992 1298 1303
-
(1992)
Science
, vol.256
, pp. 1298-1303
-
-
Herendeen, D.R.1
Kassavetis, G.A.2
Geiduschek, E.P.3
-
23
-
-
70349859881
-
DNA damage, aging, and cancer
-
J.H. Hoeijmakers DNA damage, aging, and cancer N. Engl. J. Med. 361 2009 1475 1485
-
(2009)
N. Engl. J. Med.
, vol.361
, pp. 1475-1485
-
-
Hoeijmakers, J.H.1
-
24
-
-
0018847558
-
The LNCaP cell line - A new model for studies on human prostatic carcinoma
-
J.S. Horoszewicz, S.S. Leong, T.M. Chu, Z.L. Wajsman, M. Friedman, L. Papsidero, U. Kim, L.S. Chai, S. Kakati, S.K. Arya, and A.A. Sandberg The LNCaP cell line - a new model for studies on human prostatic carcinoma Prog. Clin. Biol. Res. 37 1980 115 132
-
(1980)
Prog. Clin. Biol. Res.
, vol.37
, pp. 115-132
-
-
Horoszewicz, J.S.1
Leong, S.S.2
Chu, T.M.3
Wajsman, Z.L.4
Friedman, M.5
Papsidero, L.6
Kim, U.7
Chai, L.S.8
Kakati, S.9
Arya, S.K.10
Sandberg, A.A.11
-
25
-
-
84901020399
-
Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation
-
C.L. Hsieh, T. Fei, Y. Chen, T. Li, Y. Gao, X. Wang, T. Sun, C.J. Sweeney, G.S. Lee, and S. Chen Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation Proc. Natl. Acad. Sci. USA 111 2014 7319 7324
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 7319-7324
-
-
Hsieh, C.L.1
Fei, T.2
Chen, Y.3
Li, T.4
Gao, Y.5
Wang, X.6
Sun, T.7
Sweeney, C.J.8
Lee, G.S.9
Chen, S.10
-
26
-
-
33745255099
-
A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription
-
B.G. Ju, V.V. Lunyak, V. Perissi, I. Garcia-Bassets, D.W. Rose, C.K. Glass, and M.G. Rosenfeld A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription Science 312 2006 1798 1802
-
(2006)
Science
, vol.312
, pp. 1798-1802
-
-
Ju, B.G.1
Lunyak, V.V.2
Perissi, V.3
Garcia-Bassets, I.4
Rose, D.W.5
Glass, C.K.6
Rosenfeld, M.G.7
-
27
-
-
25444515680
-
Proteomic analysis of steady-state nuclear hormone receptor coactivator complexes
-
S.Y. Jung, A. Malovannaya, J. Wei, B.W. O'Malley, and J. Qin Proteomic analysis of steady-state nuclear hormone receptor coactivator complexes Mol. Endocrinol. 19 2005 2451 2465
-
(2005)
Mol. Endocrinol.
, vol.19
, pp. 2451-2465
-
-
Jung, S.Y.1
Malovannaya, A.2
Wei, J.3
O'Malley, B.W.4
Qin, J.5
-
28
-
-
84881526410
-
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
-
M.U. Kaikkonen, N.J. Spann, S. Heinz, C.E. Romanoski, K.A. Allison, J.D. Stender, H.B. Chun, D.F. Tough, R.K. Prinjha, C. Benner, and C.K. Glass Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription Mol. Cell 51 2013 310 325
-
(2013)
Mol. Cell
, vol.51
, pp. 310-325
-
-
Kaikkonen, M.U.1
Spann, N.J.2
Heinz, S.3
Romanoski, C.E.4
Allison, K.A.5
Stender, J.D.6
Chun, H.B.7
Tough, D.F.8
Prinjha, R.K.9
Benner, C.10
Glass, C.K.11
-
29
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
T.-K. Kim, M. Hemberg, J.M. Gray, A.M. Costa, D.M. Bear, J. Wu, D.A. Harmin, M. Laptewicz, K. Barbara-Haley, and S. Kuersten Widespread transcription at neuronal activity-regulated enhancers Nature 465 2010 182 187
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.-K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
Harmin, D.A.7
Laptewicz, M.8
Barbara-Haley, K.9
Kuersten, S.10
-
30
-
-
0032493489
-
Multiple G1 regulatory elements control the androgen-dependent proliferation of prostatic carcinoma cells
-
K.E. Knudsen, K.C. Arden, and W.K. Cavenee Multiple G1 regulatory elements control the androgen-dependent proliferation of prostatic carcinoma cells J. Biol. Chem. 273 1998 20213 20222
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 20213-20222
-
-
Knudsen, K.E.1
Arden, K.C.2
Cavenee, W.K.3
-
31
-
-
34347231949
-
Supercoil-driven DNA structures regulate genetic transactions. Frontiers in bioscience: A journal and virtual library
-
F. Kouzine, and D. Levens Supercoil-driven DNA structures regulate genetic transactions. Frontiers in bioscience: a journal and virtual library Front Biosci. 12 2007 4409 4423
-
(2007)
Front Biosci.
, vol.12
, pp. 4409-4423
-
-
Kouzine, F.1
Levens, D.2
-
32
-
-
84875185055
-
Transcription-dependent dynamic supercoiling is a short-range genomic force
-
F. Kouzine, A. Gupta, L. Baranello, D. Wojtowicz, K. Ben-Aissa, J. Liu, T.M. Przytycka, and D. Levens Transcription-dependent dynamic supercoiling is a short-range genomic force Nat. Struct. Mol. Biol. 20 2013 396 403
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 396-403
-
-
Kouzine, F.1
Gupta, A.2
Baranello, L.3
Wojtowicz, D.4
Ben-Aissa, K.5
Liu, J.6
Przytycka, T.M.7
Levens, D.8
-
33
-
-
0027138674
-
Identification of human DNA topoisomerase i as a cofactor for activator-dependent transcription by RNA polymerase II
-
M. Kretzschmar, M. Meisterernst, and R.G. Roeder Identification of human DNA topoisomerase I as a cofactor for activator-dependent transcription by RNA polymerase II Proc. Natl. Acad. Sci. USA 90 1993 11508 11512
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 11508-11512
-
-
Kretzschmar, M.1
Meisterernst, M.2
Roeder, R.G.3
-
34
-
-
0035902585
-
Single-strand interruptions in replicating chromosomes cause double-strand breaks
-
A. Kuzminov Single-strand interruptions in replicating chromosomes cause double-strand breaks Proc. Natl. Acad. Sci. USA 98 2001 8241 8246
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 8241-8246
-
-
Kuzminov, A.1
-
35
-
-
84874175008
-
Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
-
H. Kwak, N.J. Fuda, L.J. Core, and J.T. Lis Precise maps of RNA polymerase reveal how promoters direct initiation and pausing Science 339 2013 950 953
-
(2013)
Science
, vol.339
, pp. 950-953
-
-
Kwak, H.1
Fuda, N.J.2
Core, L.J.3
Lis, J.T.4
-
36
-
-
84874368349
-
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
-
F. Lai, U.A. Orom, M. Cesaroni, M. Beringer, D.J. Taatjes, G.A. Blobel, and R. Shiekhattar Activating RNAs associate with Mediator to enhance chromatin architecture and transcription Nature 494 2013 497 501
-
(2013)
Nature
, vol.494
, pp. 497-501
-
-
Lai, F.1
Orom, U.A.2
Cesaroni, M.3
Beringer, M.4
Taatjes, D.J.5
Blobel, G.A.6
Shiekhattar, R.7
-
37
-
-
0242694944
-
Werner protein stimulates topoisomerase i DNA relaxation activity
-
J.P. Laine, P.L. Opresko, F.E. Indig, J.A. Harrigan, C. von Kobbe, and V.A. Bohr Werner protein stimulates topoisomerase I DNA relaxation activity Cancer Res. 63 2003 7136 7146
-
(2003)
Cancer Res.
, vol.63
, pp. 7136-7146
-
-
Laine, J.P.1
Opresko, P.L.2
Indig, F.E.3
Harrigan, J.A.4
Von Kobbe, C.5
Bohr, V.A.6
-
38
-
-
84879694221
-
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
-
M.T. Lam, H. Cho, H.P. Lesch, D. Gosselin, S. Heinz, Y. Tanaka-Oishi, C. Benner, M.U. Kaikkonen, A.S. Kim, and M. Kosaka Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription Nature 498 2013 511 515
-
(2013)
Nature
, vol.498
, pp. 511-515
-
-
Lam, M.T.1
Cho, H.2
Lesch, H.P.3
Gosselin, D.4
Heinz, S.5
Tanaka-Oishi, Y.6
Benner, C.7
Kaikkonen, M.U.8
Kim, A.S.9
Kosaka, M.10
-
40
-
-
84865377934
-
XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes
-
N. Le May, D. Fradin, I. Iltis, P. Bougnères, and J.M. Egly XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes Mol. Cell 47 2012 622 632
-
(2012)
Mol. Cell
, vol.47
, pp. 622-632
-
-
Le May, N.1
Fradin, D.2
Iltis, I.3
Bougnères, P.4
Egly, J.M.5
-
41
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
W. Li, D. Notani, Q. Ma, B. Tanasa, E. Nunez, A.Y. Chen, D. Merkurjev, J. Zhang, K. Ohgi, and X. Song Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation Nature 498 2013 516 520
-
(2013)
Nature
, vol.498
, pp. 516-520
-
-
Li, W.1
Notani, D.2
Ma, Q.3
Tanasa, B.4
Nunez, E.5
Chen, A.Y.6
Merkurjev, D.7
Zhang, J.8
Ohgi, K.9
Song, X.10
-
42
-
-
84878218838
-
Ku80-deleted cells are defective at base excision repair
-
H. Li, T. Marple, and P. Hasty Ku80-deleted cells are defective at base excision repair Mutat. Res. 745-746 2013 16 25
-
(2013)
Mutat. Res.
, vol.745-746
, pp. 16-25
-
-
Li, H.1
Marple, T.2
Hasty, P.3
-
43
-
-
0023433855
-
Supercoiling of the DNA template during transcription
-
L.F. Liu, and J.C. Wang Supercoiling of the DNA template during transcription Proc. Natl. Acad. Sci. USA 84 1987 7024 7027
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 7024-7027
-
-
Liu, L.F.1
Wang, J.C.2
-
44
-
-
84902385349
-
Interplay between DNA supercoiling and transcription elongation
-
Published online April 7, 2014
-
J. Ma, and M. Wang Interplay between DNA supercoiling and transcription elongation Transcription 5 2014 Published online April 7, 2014
-
(2014)
Transcription
, vol.5
-
-
Ma, J.1
Wang, M.2
-
45
-
-
0026503077
-
Overexpression of human topoisomerase i in baby hamster kidney cells: Hypersensitivity of clonal isolates to camptothecin
-
K.R. Madden, and J.J. Champoux Overexpression of human topoisomerase I in baby hamster kidney cells: hypersensitivity of clonal isolates to camptothecin Cancer Res. 52 1992 525 532
-
(1992)
Cancer Res.
, vol.52
, pp. 525-532
-
-
Madden, K.R.1
Champoux, J.J.2
-
46
-
-
15844390393
-
A human RNA polymerase II complex associated with SRB and DNA-repair proteins
-
E. Maldonado, R. Shiekhattar, M. Sheldon, H. Cho, R. Drapkin, P. Rickert, E. Lees, C.W. Anderson, S. Linn, and D. Reinberg A human RNA polymerase II complex associated with SRB and DNA-repair proteins Nature 381 1996 86 89
-
(1996)
Nature
, vol.381
, pp. 86-89
-
-
Maldonado, E.1
Shiekhattar, R.2
Sheldon, M.3
Cho, H.4
Drapkin, R.5
Rickert, P.6
Lees, E.7
Anderson, C.W.8
Linn, S.9
Reinberg, D.10
-
47
-
-
15444375185
-
Ku is a novel transcriptional recycling coactivator of the androgen receptor in prostate cancer cells
-
G.L. Mayeur, W.J. Kung, A. Martinez, C. Izumiya, D.J. Chen, and H.J. Kung Ku is a novel transcriptional recycling coactivator of the androgen receptor in prostate cancer cells J. Biol. Chem. 280 2005 10827 10833
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 10827-10833
-
-
Mayeur, G.L.1
Kung, W.J.2
Martinez, A.3
Izumiya, C.4
Chen, D.J.5
Kung, H.J.6
-
48
-
-
81055126951
-
Discovery of active enhancers through bidirectional expression of short transcripts
-
M.F. Melgar, F.S. Collins, and P. Sethupathy Discovery of active enhancers through bidirectional expression of short transcripts Genome Biol. 12 2011 R113
-
(2011)
Genome Biol.
, vol.12
, pp. R113
-
-
Melgar, M.F.1
Collins, F.S.2
Sethupathy, P.3
-
49
-
-
84873456575
-
ERNAs are required for p53-dependent enhancer activity and gene transcription
-
C.A. Melo, J. Drost, P.J. Wijchers, H. van de Werken, E. de Wit, J.A. Oude Vrielink, R. Elkon, S.A. Melo, N. Léveillé, and R. Kalluri eRNAs are required for p53-dependent enhancer activity and gene transcription Mol. Cell 49 2013 524 535
-
(2013)
Mol. Cell
, vol.49
, pp. 524-535
-
-
Melo, C.A.1
Drost, J.2
Wijchers, P.J.3
Van De Werken, H.4
De Wit, E.5
Oude Vrielink, J.A.6
Elkon, R.7
Melo, S.A.8
Léveillé, N.9
Kalluri, R.10
-
50
-
-
0027186443
-
DNA topoisomerase i is involved in both repression and activation of transcription
-
A. Merino, K.R. Madden, W.S. Lane, J.J. Champoux, and D. Reinberg DNA topoisomerase I is involved in both repression and activation of transcription Nature 365 1993 227 232
-
(1993)
Nature
, vol.365
, pp. 227-232
-
-
Merino, A.1
Madden, K.R.2
Lane, W.S.3
Champoux, J.J.4
Reinberg, D.5
-
51
-
-
0036839642
-
Subnuclear localization of Ku protein: Functional association with RNA polymerase II elongation sites
-
X. Mo, and W.S. Dynan Subnuclear localization of Ku protein: functional association with RNA polymerase II elongation sites Mol. Cell. Biol. 22 2002 8088 8099
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 8088-8099
-
-
Mo, X.1
Dynan, W.S.2
-
52
-
-
84883756441
-
ERNAs promote transcription by establishing chromatin accessibility at defined genomic loci
-
K. Mousavi, H. Zare, S. Dell'orso, L. Grontved, G. Gutierrez-Cruz, A. Derfoul, G.L. Hager, and V. Sartorelli eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci Mol. Cell 51 2013 606 617
-
(2013)
Mol. Cell
, vol.51
, pp. 606-617
-
-
Mousavi, K.1
Zare, H.2
Dell'Orso, S.3
Grontved, L.4
Gutierrez-Cruz, G.5
Derfoul, A.6
Hager, G.L.7
Sartorelli, V.8
-
53
-
-
84870182699
-
Noncoding transcription at enhancers: General principles and functional models
-
G. Natoli, and J.-C. Andrau Noncoding transcription at enhancers: general principles and functional models Annu. Rev. Genet. 46 2012 1 19
-
(2012)
Annu. Rev. Genet.
, vol.46
, pp. 1-19
-
-
Natoli, G.1
Andrau, J.-C.2
-
54
-
-
79951688343
-
BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair
-
A.V. Nimonkar, J. Genschel, E. Kinoshita, P. Polaczek, J.L. Campbell, C. Wyman, P. Modrich, and S.C. Kowalczykowski BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair Genes Dev. 25 2011 350 362
-
(2011)
Genes Dev.
, vol.25
, pp. 350-362
-
-
Nimonkar, A.V.1
Genschel, J.2
Kinoshita, E.3
Polaczek, P.4
Campbell, J.L.5
Wyman, C.6
Modrich, P.7
Kowalczykowski, S.C.8
-
55
-
-
84872011816
-
DNA topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae
-
J.M. Pedersen, J. Fredsoe, M. Roedgaard, L. Andreasen, K. Mundbjerg, M. Kruhøffer, M. Brinch, M.H. Schierup, L. Bjergbaek, and A.H. Andersen DNA topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae PLoS Genet. 8 2012 e1003128
-
(2012)
PLoS Genet.
, vol.8
, pp. e1003128
-
-
Pedersen, J.M.1
Fredsoe, J.2
Roedgaard, M.3
Andreasen, L.4
Mundbjerg, K.5
Kruhøffer, M.6
Brinch, M.7
Schierup, M.H.8
Bjergbaek, L.9
Andersen, A.H.10
-
56
-
-
84875156063
-
Enhancers: Five essential questions
-
L.A. Pennacchio, W. Bickmore, A. Dean, M.A. Nobrega, and G. Bejerano Enhancers: five essential questions Nat. Rev. Genet. 14 2013 288 295
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 288-295
-
-
Pennacchio, L.A.1
Bickmore, W.2
Dean, A.3
Nobrega, M.A.4
Bejerano, G.5
-
57
-
-
84887419126
-
Androgen receptor signaling regulates DNA repair in prostate cancers
-
W.R. Polkinghorn, J.S. Parker, M.X. Lee, E.M. Kass, D.E. Spratt, P.J. Iaquinta, V.K. Arora, W.F. Yen, L. Cai, and D. Zheng Androgen receptor signaling regulates DNA repair in prostate cancers Cancer Discov. 3 2013 1245 1253
-
(2013)
Cancer Discov.
, vol.3
, pp. 1245-1253
-
-
Polkinghorn, W.R.1
Parker, J.S.2
Lee, M.X.3
Kass, E.M.4
Spratt, D.E.5
Iaquinta, P.J.6
Arora, V.K.7
Yen, W.F.8
Cai, L.9
Zheng, D.10
-
58
-
-
0032189683
-
Mechanism of action of eukaryotic DNA topoisomerase i and drugs targeted to the enzyme
-
Y. Pommier, P. Pourquier, Y. Fan, and D. Strumberg Mechanism of action of eukaryotic DNA topoisomerase I and drugs targeted to the enzyme Biochim. Biophys. Acta 1400 1998 83 105
-
(1998)
Biochim. Biophys. Acta
, vol.1400
, pp. 83-105
-
-
Pommier, Y.1
Pourquier, P.2
Fan, Y.3
Strumberg, D.4
-
59
-
-
33745278845
-
Repair of topoisomerase I-mediated DNA damage
-
Y. Pommier, J.M. Barcelo, V.A. Rao, O. Sordet, A.G. Jobson, L. Thibaut, Z.H. Miao, J.A. Seiler, H. Zhang, and C. Marchand Repair of topoisomerase I-mediated DNA damage Prog. Nucleic Acid Res. Mol. Biol. 81 2006 179 229
-
(2006)
Prog. Nucleic Acid Res. Mol. Biol.
, vol.81
, pp. 179-229
-
-
Pommier, Y.1
Barcelo, J.M.2
Rao, V.A.3
Sordet, O.4
Jobson, A.G.5
Thibaut, L.6
Miao, Z.H.7
Seiler, J.A.8
Zhang, H.9
Marchand, C.10
-
60
-
-
77954187741
-
DNA topoisomerases and their poisoning by anticancer and antibacterial drugs
-
Y. Pommier, E. Leo, H. Zhang, and C. Marchand DNA topoisomerases and their poisoning by anticancer and antibacterial drugs Chem. Biol. 17 2010 421 433
-
(2010)
Chem. Biol.
, vol.17
, pp. 421-433
-
-
Pommier, Y.1
Leo, E.2
Zhang, H.3
Marchand, C.4
-
61
-
-
84904248751
-
Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms
-
C.J. Potenski, H. Niu, P. Sung, and H.L. Klein Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms Nature 511 2014 251 254
-
(2014)
Nature
, vol.511
, pp. 251-254
-
-
Potenski, C.J.1
Niu, H.2
Sung, P.3
Klein, H.L.4
-
62
-
-
84875198804
-
Chromatin remodeling at DNA double-strand breaks
-
B.D. Price, and A.D. D'Andrea Chromatin remodeling at DNA double-strand breaks Cell 152 2013 1344 1354
-
(2013)
Cell
, vol.152
, pp. 1344-1354
-
-
Price, B.D.1
D'Andrea, A.D.2
-
63
-
-
84455192646
-
DNA repair factor MRE11/RAD50 cleaves 3′-phosphotyrosyl bonds and resects DNA to repair damage caused by topoisomerase 1 poisons
-
E.J. Sacho, and N. Maizels DNA repair factor MRE11/RAD50 cleaves 3′-phosphotyrosyl bonds and resects DNA to repair damage caused by topoisomerase 1 poisons J. Biol. Chem. 286 2011 44945 44951
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 44945-44951
-
-
Sacho, E.J.1
Maizels, N.2
-
64
-
-
84899450857
-
Transcriptional enhancers: From properties to genome-wide predictions
-
D. Shlyueva, G. Stampfel, and A. Stark Transcriptional enhancers: from properties to genome-wide predictions Nat. Rev. Genet. 15 2014 272 286
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 272-286
-
-
Shlyueva, D.1
Stampfel, G.2
Stark, A.3
-
65
-
-
0031049483
-
Topoisomerase i enhances TFIID-TFIIA complex assembly during activation of transcription
-
B.M. Shykind, J. Kim, L. Stewart, J.J. Champoux, and P.A. Sharp Topoisomerase I enhances TFIID-TFIIA complex assembly during activation of transcription Genes Dev. 11 1997 397 407
-
(1997)
Genes Dev.
, vol.11
, pp. 397-407
-
-
Shykind, B.M.1
Kim, J.2
Stewart, L.3
Champoux, J.J.4
Sharp, P.A.5
-
66
-
-
0032493634
-
The activity of topoisomerase i is modulated by large T antigen during unwinding of the SV40 origin
-
D.T. Simmons, R. Roy, L. Chen, D. Gai, and P.W. Trowbridge The activity of topoisomerase I is modulated by large T antigen during unwinding of the SV40 origin J. Biol. Chem. 273 1998 20390 20396
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 20390-20396
-
-
Simmons, D.T.1
Roy, R.2
Chen, L.3
Gai, D.4
Trowbridge, P.W.5
-
67
-
-
84892728434
-
Sequencing depth and coverage: Key considerations in genomic analyses
-
D. Sims, I. Sudbery, N.E. Ilott, A. Heger, and C.P. Ponting Sequencing depth and coverage: key considerations in genomic analyses Nat. Rev. Genet. 15 2014 121 132
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 121-132
-
-
Sims, D.1
Sudbery, I.2
Ilott, N.E.3
Heger, A.4
Ponting, C.P.5
-
68
-
-
0032489675
-
A model for the mechanism of human topoisomerase i
-
L. Stewart, M.R. Redinbo, X. Qiu, W.G. Hol, and J.J. Champoux A model for the mechanism of human topoisomerase I Science 279 1998 1534 1541
-
(1998)
Science
, vol.279
, pp. 1534-1541
-
-
Stewart, L.1
Redinbo, M.R.2
Qiu, X.3
Hol, W.G.4
Champoux, J.J.5
-
70
-
-
84863072810
-
Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival
-
P.Y. Tan, C.W. Chang, K.R. Chng, K.D. Wansa, W.K. Sung, and E. Cheung Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival Mol. Cell. Biol. 32 2012 399 414
-
(2012)
Mol. Cell. Biol.
, vol.32
, pp. 399-414
-
-
Tan, P.Y.1
Chang, C.W.2
Chng, K.R.3
Wansa, K.D.4
Sung, W.K.5
Cheung, E.6
-
71
-
-
0027139317
-
Interaction between replication forks and topoisomerase I-DNA cleavable complexes: Studies in a cell-free SV40 DNA replication system
-
Y.P. Tsao, A. Russo, G. Nyamuswa, R. Silber, and L.F. Liu Interaction between replication forks and topoisomerase I-DNA cleavable complexes: studies in a cell-free SV40 DNA replication system Cancer Res. 53 1993 5908 5914
-
(1993)
Cancer Res.
, vol.53
, pp. 5908-5914
-
-
Tsao, Y.P.1
Russo, A.2
Nyamuswa, G.3
Silber, R.4
Liu, L.F.5
-
72
-
-
79959198166
-
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
-
D. Wang, I. Garcia-Bassets, C. Benner, W. Li, X. Su, Y. Zhou, J. Qiu, W. Liu, M.U. Kaikkonen, and K.A. Ohgi Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA Nature 474 2011 390 394
-
(2011)
Nature
, vol.474
, pp. 390-394
-
-
Wang, D.1
Garcia-Bassets, I.2
Benner, C.3
Li, W.4
Su, X.5
Zhou, Y.6
Qiu, J.7
Liu, W.8
Kaikkonen, M.U.9
Ohgi, K.A.10
-
73
-
-
84881342072
-
R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli
-
H. Wimberly, C. Shee, P.C. Thornton, P. Sivaramakrishnan, S.M. Rosenberg, and P.J. Hastings R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli Nat. Commun. 4 2013 2115
-
(2013)
Nat. Commun.
, vol.4
, pp. 2115
-
-
Wimberly, H.1
Shee, C.2
Thornton, P.C.3
Sivaramakrishnan, P.4
Rosenberg, S.M.5
Hastings, P.J.6
-
74
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
N.D. Heintzman, G.C. Hon, R.D. Hawkins, P. Kheradpour, A. Stark, L.F. Harp, Z. Ye, L.K. Lee, R.K. Stuart, and C.W. Ching Histone modifications at human enhancers reflect global cell-type-specific gene expression Nature 459 2009 108 112
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
Harp, L.F.6
Ye, Z.7
Lee, L.K.8
Stuart, R.K.9
Ching, C.W.10
-
75
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
S. Heinz, C. Benner, N. Spann, E. Bertolino, Y.C. Lin, P. Laslo, J.X. Cheng, C. Murre, H. Singh, and C.K. Glass Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities Mol. Cell 38 2010 576 589
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
76
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
N. Homer, B. Merriman, and S.F. Nelson BFAST: an alignment tool for large scale genome resequencing PLoS ONE 4 2009 e7767
-
(2009)
PLoS ONE
, vol.4
, pp. e7767
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
77
-
-
84871808580
-
Binary Interval Search: A scalable algorithm for counting interval intersections
-
R.M. Layer, K. Skadron, G. Robins, I.M. Hall, and A.R. Quinlan Binary Interval Search: a scalable algorithm for counting interval intersections Bioinformatics 29 2013 1 7
-
(2013)
Bioinformatics
, vol.29
, pp. 1-7
-
-
Layer, R.M.1
Skadron, K.2
Robins, G.3
Hall, I.M.4
Quinlan, A.R.5
-
78
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
W. Li, D. Notani, Q. Ma, B. Tanasa, E. Nunez, A.Y. Chen, D. Merkurjev, J. Zhang, K. Ohgi, and X. Song Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation Nature 498 2013 516 520
-
(2013)
Nature
, vol.498
, pp. 516-520
-
-
Li, W.1
Notani, D.2
Ma, Q.3
Tanasa, B.4
Nunez, E.5
Chen, A.Y.6
Merkurjev, D.7
Zhang, J.8
Ohgi, K.9
Song, X.10
-
79
-
-
84916897361
-
Enhancer activation requires trans-recruitment of a mega transcription factor complex
-
Z. Liu, D. Merkurjev, F. Yang, W. Li, S. Oh, M.J. Friedman, X. Song, F. Zhang, Q. Ma, and K.A. Ohgi Enhancer activation requires trans-recruitment of a mega transcription factor complex Cell 159 2014 358 373
-
(2014)
Cell
, vol.159
, pp. 358-373
-
-
Liu, Z.1
Merkurjev, D.2
Yang, F.3
Li, W.4
Oh, S.5
Friedman, M.J.6
Song, X.7
Zhang, F.8
Ma, Q.9
Ohgi, K.A.10
-
80
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
81
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
C. Zang, D.E. Schones, C. Zeng, K. Cui, K. Zhao, and W. Peng A clustering approach for identification of enriched domains from histone modification ChIP-Seq data Bioinformatics 25 2009 1952 1958
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.E.2
Zeng, C.3
Cui, K.4
Zhao, K.5
Peng, W.6
-
82
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nusbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
|