-
1
-
-
84881166117
-
Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes
-
Narlikar, G. J., Sundaramoorthy, R. & Owen-Hughes, T. Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154, 490-503 (2013).
-
(2013)
Cell
, vol.154
, pp. 490-503
-
-
Narlikar, G.J.1
Sundaramoorthy, R.2
Owen-Hughes, T.3
-
2
-
-
0027474628
-
A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain
-
Delmas, V., Stokes, D. G. & Perry, R. P. A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain. Proc. Natl Acad. Sci. USA 90, 2414-2418 (1993).
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 2414-2418
-
-
Delmas, V.1
Stokes, D.G.2
Perry, R.P.3
-
3
-
-
84929207966
-
Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density
-
Lieleg, C. et al. Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density. Mol. Cell. Biol. 35, 1588-1605 (2015).
-
(2015)
Mol. Cell. Biol
, vol.35
, pp. 1588-1605
-
-
Lieleg, C.1
-
4
-
-
84940862471
-
Comparative genomics reveals Chd1 as a determinant of nucleosome spacing in vivo
-
Hughes, A. L. & Rando, O. J. Comparative genomics reveals Chd1 as a determinant of nucleosome spacing in vivo. G3 (Bethesda) 5, 1889-1897 (2015).
-
(2015)
G3 (Bethesda)
, vol.5
, pp. 1889-1897
-
-
Hughes, A.L.1
Rando, O.J.2
-
5
-
-
15544369061
-
Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly
-
Lusser, A., Urwin, D. L. & Kadonaga, J. T. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12, 160-166 (2005).
-
(2005)
Nat. Struct. Mol. Biol
, vol.12
, pp. 160-166
-
-
Lusser, A.1
Urwin, D.L.2
Kadonaga, J.T.3
-
6
-
-
84899620204
-
The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1
-
Skene, P. J., Hernandez, A. E., Groudine, M. & Henikoff, S. The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. eLife 3, e02042 (2014).
-
(2014)
ELife
, vol.3
, pp. e02042
-
-
Skene, P.J.1
Hernandez, A.E.2
Groudine, M.3
Henikoff, S.4
-
7
-
-
68949164755
-
Chd1 regulates open chromatin and pluripotency of embryonic stem cells
-
Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863-868 (2009).
-
(2009)
Nature
, vol.460
, pp. 863-868
-
-
Gaspar-Maia, A.1
-
8
-
-
85018736844
-
Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure
-
Liu, X., Li, M., Xia, X., Li, X. & Chen, Z. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature 544, 440-445 (2017).
-
(2017)
Nature
, vol.544
, pp. 440-445
-
-
Liu, X.1
Li, M.2
Xia, X.3
Li, X.4
Chen, Z.5
-
9
-
-
85009804160
-
Interdomain communication of the Chd1 chromatin remodeler across the DNA gyres of the nucleosome
-
Nodelman, I. M. et al. Interdomain communication of the Chd1 chromatin remodeler across the DNA gyres of the nucleosome. Mol. Cell 65, 447-459.e6 (2017).
-
(2017)
Mol. Cell
, vol.65
, pp. 447-447e6
-
-
Nodelman, I.M.1
-
10
-
-
0032512794
-
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
-
Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19-42 (1998).
-
(1998)
J. Mol. Biol
, vol.276
, pp. 19-42
-
-
Lowary, P.T.1
Widom, J.2
-
11
-
-
77957252758
-
Crystal structures of nucleosome core particles containing the 601 strong positioning sequence
-
Vasudevan, D., Chua, E. Y. D. & Davey, C. A. Crystal structures of nucleosome core particles containing the 601 strong positioning sequence. J. Mol. Biol. 403, 1-10 (2010).
-
(2010)
J. Mol. Biol
, vol.403
, pp. 1-10
-
-
Vasudevan, D.1
Chua, E.Y.D.2
Davey, C.A.3
-
12
-
-
77956522905
-
The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor
-
Hauk, G., McKnight, J. N., Nodelman, I. M. & Bowman, G. D. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol. Cell 39, 711-723 (2010).
-
(2010)
Mol. Cell
, vol.39
, pp. 711-723
-
-
Hauk, G.1
McKnight, J.N.2
Nodelman, I.M.3
Bowman, G.D.4
-
13
-
-
82755183623
-
Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA
-
Sharma, A., Jenkins, K. R., Héroux, A. & Bowman, G. D. Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J. Biol. Chem. 286, 42099-42104 (2011).
-
(2011)
J. Biol. Chem
, vol.286
, pp. 42099-42104
-
-
Sharma, A.1
Jenkins, K.R.2
Héroux, A.3
Bowman, G.D.4
-
14
-
-
84991706628
-
The chromatin remodelling protein CHD1 contains a previously unrecognised C-Terminal helical domain
-
Mohanty, B., Helder, S., Silva, A. P. G., Mackay, J. P. & Ryan, D. P. The chromatin remodelling protein CHD1 contains a previously unrecognised C-Terminal helical domain. J. Mol. Biol. 428, 4298-4314 (2016).
-
(2016)
J. Mol. Biol
, vol.428
, pp. 4298-4314
-
-
Mohanty, B.1
Helder, S.2
Silva, A.P.G.3
Mackay, J.P.4
Ryan, D.P.5
-
15
-
-
85017511461
-
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
-
Sundaramoorthy, R. et al. Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife 6, e22510-e22528 (2017).
-
(2017)
ELife
, vol.6
, pp. e22510-e22528
-
-
Sundaramoorthy, R.1
-
16
-
-
85010645289
-
Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler
-
Sinha, K. K., Gross, J. D. & Narlikar, G. J. Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler. Science 355, eaaa3761 (2017).
-
(2017)
Science
, vol.355
, pp. eaaa3761
-
-
Sinha, K.K.1
Gross, J.D.2
Narlikar, G.J.3
-
17
-
-
83255185775
-
Extranucleosomal DNA binding directs nucleosome sliding by Chd1
-
McKnight, J. N., Jenkins, K. R., Nodelman, I. M., Escobar, T. & Bowman, G. D. Extranucleosomal DNA binding directs nucleosome sliding by Chd1. Mol. Cell. Biol. 31, 4746-4759 (2011).
-
(2011)
Mol. Cell. Biol
, vol.31
, pp. 4746-4759
-
-
McKnight, J.N.1
Jenkins, K.R.2
Nodelman, I.M.3
Escobar, T.4
Bowman, G.D.5
-
18
-
-
85018756382
-
Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1
-
Bednar, J. et al. Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1. Mol. Cell 66, 384-397.e8 (2017).
-
(2017)
Mol. Cell
, vol.66
, pp. 384-384e8
-
-
Bednar, J.1
-
19
-
-
76249111702
-
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
-
Gu, M. & Rice, C. M. Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc. Natl Acad. Sci. USA 107, 521-528 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 521-528
-
-
Gu, M.1
Rice, C.M.2
-
20
-
-
33646017369
-
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
-
Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S. & Yokoyama, S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125, 287-300 (2006).
-
(2006)
Cell
, vol.125
, pp. 287-300
-
-
Sengoku, T.1
Nureki, O.2
Nakamura, A.3
Kobayashi, S.4
Yokoyama, S.5
-
21
-
-
84866390624
-
Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness
-
Huang, S. et al. Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness. Oncogene 31, 4164-4170 (2012).
-
(2012)
Oncogene
, vol.31
, pp. 4164-4170
-
-
Huang, S.1
-
22
-
-
34548638261
-
Structure and mechanism of helicases and nucleic acid translocases
-
Singleton, M. R., Dillingham, M. S. & Wigley, D. B. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76, 23-50 (2007).
-
(2007)
Annu. Rev. Biochem
, vol.76
, pp. 23-50
-
-
Singleton, M.R.1
Dillingham, M.S.2
Wigley, D.B.3
-
23
-
-
18844457346
-
X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA
-
Dörr, H., Körner, C., Möller, M., Hickmann, V. & Hopfner, K.-P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121, 363-373 (2005).
-
(2005)
Cell
, vol.121
, pp. 363-373
-
-
Dörr, H.1
Körner, C.2
Möller, M.3
Hickmann, V.4
Hopfner, K.-P.5
-
24
-
-
26944461283
-
Chromatin remodeling through directional DNA translocation from an internal nucleosomal site
-
Saha, A., Wittmeyer, J. & Cairns, B. R. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12, 747-755 (2005).
-
(2005)
Nat. Struct. Mol. Biol
, vol.12
, pp. 747-755
-
-
Saha, A.1
Wittmeyer, J.2
Cairns, B.R.3
-
25
-
-
66149148295
-
Mechanistic basis of 5′-3′ translocation in SF1B helicases
-
Saikrishnan, K., Powell, B., Cook, N. J., Webb, M. R. & Wigley, D. B. Mechanistic basis of 5′-3′ translocation in SF1B helicases. Cell 137, 849-859 (2009).
-
(2009)
Cell
, vol.137
, pp. 849-859
-
-
Saikrishnan, K.1
Powell, B.2
Cook, N.J.3
Webb, M.R.4
Wigley, D.B.5
-
26
-
-
33846936301
-
Mechanisms of nucleic acid translocases: Lessons from structural biology and single-molecule biophysics
-
Hopfner, K.-P. & Michaelis, J. Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics. Curr. Opin. Struct. Biol. 17, 87-95 (2007).
-
(2007)
Curr. Opin. Struct. Biol
, vol.17
, pp. 87-95
-
-
Hopfner, K.-P.1
Michaelis, J.2
-
28
-
-
84870532434
-
Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes
-
Le Gallo, M. et al. Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nat. Genet. 44, 1310-1315 (2012).
-
(2012)
Nat. Genet
, vol.44
, pp. 1310-1315
-
-
Le Gallo, M.1
-
29
-
-
0035137666
-
Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI
-
Clapier, C. R., Längst, G., Corona, D. F., Becker, P. B. & Nightingale, K. P. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21, 875-883 (2001).
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 875-883
-
-
Clapier, C.R.1
Längst, G.2
Corona, D.F.3
Becker, P.B.4
Nightingale, K.P.5
-
30
-
-
84988921966
-
The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome
-
Nodelman, I. M. et al. The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome. Nucleic Acids Res. 44, 7580-7591 (2016).
-
(2016)
Nucleic Acids Res
, vol.44
, pp. 7580-7591
-
-
Nodelman, I.M.1
-
31
-
-
67650725820
-
The biology of chromatin remodeling complexes
-
Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304 (2009).
-
(2009)
Annu. Rev. Biochem
, vol.78
, pp. 273-304
-
-
Clapier, C.R.1
Cairns, B.R.2
-
32
-
-
84924041052
-
A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler
-
Leonard, J. D. & Narlikar, G. J. A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler. Mol. Cell 57, 850-859 (2015).
-
(2015)
Mol. Cell
, vol.57
, pp. 850-859
-
-
Leonard, J.D.1
Narlikar, G.J.2
-
33
-
-
85016142239
-
Structure and regulation of the chromatin remodeller ISWI
-
Yan, L., Wang, L., Tian, Y., Xia, X. & Chen, Z. Structure and regulation of the chromatin remodeller ISWI. Nature 540, 466-469 (2016).
-
(2016)
Nature
, vol.540
, pp. 466-469
-
-
Yan, L.1
Wang, L.2
Tian, Y.3
Xia, X.4
Chen, Z.5
-
34
-
-
85020418489
-
Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex
-
Xu, Y. et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nat. Commun. 8, 15741 (2017).
-
(2017)
Nat. Commun
, vol.8
, pp. 15741
-
-
Xu, Y.1
-
35
-
-
84978832727
-
Architecture and RNA binding of the human negative elongation factor
-
Vos, S. M. et al. Architecture and RNA binding of the human negative elongation factor. eLife 5, e14981 (2016).
-
(2016)
ELife
, vol.5
, pp. e14981
-
-
Vos, S.M.1
-
36
-
-
0033289822
-
Expression and purification of recombinant histones and nucleosome reconstitution
-
Luger, K., Rechsteiner, T. J. & Richmond, T. J. Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1-16 (1999).
-
(1999)
Methods Mol. Biol
, vol.119
, pp. 1-16
-
-
Luger, K.1
Rechsteiner, T.J.2
Richmond, T.J.3
-
37
-
-
1542334851
-
Reconstitution of nucleosome core particles from recombinant histones and DNA
-
Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23-44 (2003).
-
(2003)
Methods Enzymol
, vol.375
, pp. 23-44
-
-
Dyer, P.N.1
-
38
-
-
84928916966
-
Structural basis for retroviral integration into nucleosomes
-
Maskell, D. P. et al. Structural basis for retroviral integration into nucleosomes. Nature 523, 366-369 (2015).
-
(2015)
Nature
, vol.523
, pp. 366-369
-
-
Maskell, D.P.1
-
39
-
-
85014129582
-
MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy
-
Zheng, S. Q. et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331-332 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 331-332
-
-
Zheng, S.Q.1
-
40
-
-
84955216953
-
Gctf: Real-Time CTF determination and correction
-
Zhang, K. Gctf: Real-Time CTF determination and correction. J. Struct. Biol. 193, 1-12 (2016).
-
(2016)
J. Struct. Biol
, vol.193
, pp. 1-12
-
-
Zhang, K.1
-
41
-
-
84855818650
-
A Bayesian view on cryo-EM structure determination
-
Scheres, S. H. W. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406-418 (2012).
-
(2012)
J. Mol. Biol
, vol.415
, pp. 406-418
-
-
Scheres, S.H.W.1
-
42
-
-
85009208040
-
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
-
Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife 5, e18722 (2016).
-
(2016)
ELife
, vol.5
, pp. e18722
-
-
Kimanius, D.1
Forsberg, B.O.2
Scheres, S.H.3
Lindahl, E.4
-
43
-
-
84970976578
-
Transcription initiation complex structures elucidate DNA opening
-
Plaschka, C. et al. Transcription initiation complex structures elucidate DNA opening. Nature 533, 353-358 (2016).
-
(2016)
Nature
, vol.533
, pp. 353-358
-
-
Plaschka, C.1
-
44
-
-
4444221565
-
UCSF Chimera-A visualization system for exploratory research and analysis
-
Pettersen, E. F. et al. UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
-
45
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486-501 (2010).
-
(2010)
Acta Crystallogr D
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
46
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996).
-
(1996)
J. Mol. Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
47
-
-
42949089487
-
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
-
Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673-683 (2008).
-
(2008)
Structure
, vol.16
, pp. 673-683
-
-
Trabuco, L.G.1
Villa, E.2
Mitra, K.3
Frank, J.4
Schulten, K.5
-
48
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
-
(2010)
Acta Crystallogr
, Issue.66
, pp. 213-221
-
-
Adams, P.D.1
-
49
-
-
70350344051
-
Running in reverse: The structural basis for translocation polarity in hexameric helicases
-
Thomsen, N. D. & Berger, J. M. Running in reverse: The structural basis for translocation polarity in hexameric helicases. Cell 139, 523-534 (2009).
-
(2009)
Cell
, vol.139
, pp. 523-534
-
-
Thomsen, N.D.1
Berger, J.M.2
-
51
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
52
-
-
65449188232
-
Jalview Version 2-A multiple sequence alignment editor and analysis workbench
-
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189-1191 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.A.3
Clamp, M.4
Barton, G.J.5
|