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Volumn 5, Issue APRIL2016, 2016, Pages

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

Author keywords

[No Author keywords available]

Indexed keywords

BREATHING; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DNA SEQUENCE; NUCLEOSOME; ANIMAL; CRISPR CAS SYSTEM; GENE EDITING; GENETIC RECOMBINATION; METABOLISM; PROCEDURES; XENOPUS;

EID: 84971539053     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.13450     Document Type: Article
Times cited : (160)

References (50)
  • 1
    • 84925456214 scopus 로고    scopus 로고
    • Chapter One - In Vitro Enzymology of Cas9
    • Doudna JA, Sontheimer EJ, Academic Press
    • Anders C, Jinek M. 2014. Chapter One - In Vitro Enzymology of Cas9. In: Doudna JA, Sontheimer EJ. Methods in Enzymology. Academic Press 546:1–20. doi: 10.1016/B978-0-12-801185-0.00001-5
    • (2014) Methods in Enzymology , vol.546 , pp. 1-20
    • Anders, C.1    Jinek, M.2
  • 2
    • 0036786970 scopus 로고    scopus 로고
    • Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation
    • Anderson JD, Tha°stro¨m A, Widom J. 2002. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Molecular and Cellular Biology 22: 7147–7157. doi: 10.1128/MCB.22.20.7147-7157.2002
    • (2002) Molecular and Cellular Biology , vol.22 , pp. 7147-7157
    • Anderson, J.D.1    Tha°stro¨m, A.2    Widom, J.3
  • 3
    • 0034598944 scopus 로고    scopus 로고
    • Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites
    • Anderson JD, Widom J. 2000. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. Journal of Molecular Biology 296:979–987. doi: 10.1006/jmbi.2000.3531
    • (2000) Journal of Molecular Biology , vol.296 , pp. 979-987
    • Anderson, J.D.1    Widom, J.2
  • 5
    • 67650725820 scopus 로고    scopus 로고
    • The biology of chromatin remodeling complexes
    • Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annual Review of Biochemistry 78:273–304. doi: 10.1146/annurev.biochem.77.062706.153223
    • (2009) Annual Review of Biochemistry , vol.78 , pp. 273-304
    • Clapier, C.R.1    Cairns, B.R.2
  • 7
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380. doi: 10.1038/nature11082
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 8
    • 84913594397 scopus 로고    scopus 로고
    • The new frontier of genome engineering with crispr-cas9
    • Doudna JA, Charpentier E. 2014. The new frontier of genome engineering with crispr-cas9. Science 346: 1258096. doi: 10.1126/science.1258096
    • (2014) Science , vol.346
    • Doudna, J.A.1    Charpentier, E.2
  • 11
    • 0028947749 scopus 로고
    • The effects of 5-azacytidine and 5-azadeoxycytidine on chromosome structure and function: Implications for methylation-associated cellular processes
    • Haaf T. 1995. The effects of 5-azacytidine and 5-azadeoxycytidine on chromosome structure and function: Implications for methylation-associated cellular processes. Pharmacology & Therapeutics 65:19–46. doi: 10.1016/0163-7258(94)00053-6
    • (1995) Pharmacology & Therapeutics , vol.65 , pp. 19-46
    • Haaf, T.1
  • 13
    • 84949032804 scopus 로고    scopus 로고
    • Nucleosomes inhibit cas9 endonuclease activity in vitro
    • Hinz JM, Laughery MF, Wyrick JJ. 2015. Nucleosomes inhibit cas9 endonuclease activity in vitro. Biochemistry 54:7063–7066. doi: 10.1021/acs.biochem.5b01108
    • (2015) Biochemistry , vol.54 , pp. 7063-7066
    • Hinz, J.M.1    Laughery, M.F.2    Wyrick, J.J.3
  • 15
    • 84934435162 scopus 로고    scopus 로고
    • Mapping nucleosome resolution chromosome folding in yeast by micro-c
    • Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ, Friedman N. 2015. Mapping nucleosome resolution chromosome folding in yeast by micro-c. Cell 162:108–119. doi: 10.1016/j.cell.2015.05.048
    • (2015) Cell , vol.162 , pp. 108-119
    • Hsieh, T.H.1    Weiner, A.2    Lajoie, B.3    Dekker, J.4    Friedman, N.5    Rando, O.J.6    Friedman, N.7
  • 16
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • Jiang C, Pugh BF. 2009. Nucleosome positioning and gene regulation: Advances through genomics. Nature Reviews. Genetics 10:161–172. doi: 10.1038/nrg2522
    • (2009) Nature Reviews. Genetics , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 17
    • 84933574487 scopus 로고    scopus 로고
    • A cas9-guide RNA complex preorganized for target DNA recognition
    • Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. 2015. A cas9-guide RNA complex preorganized for target DNA recognition. Science 348:1477–1481. doi: 10.1126/science.aab1452
    • (2015) Science , vol.348 , pp. 1477-1481
    • Jiang, F.1    Zhou, K.2    Ma, L.3    Gressel, S.4    Doudna, J.A.5
  • 18
    • 84865070369 scopus 로고    scopus 로고
    • A programmable dual-rna-guided DNA endonuclease in adaptive bacterial immunity
    • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-rna-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. doi: 10.1126/science.1225829
    • (2012) Science , vol.337 , pp. 816-821
    • Jinek, M.1    Chylinski, K.2    Fonfara, I.3    Hauer, M.4    Doudna, J.A.5    Charpentier, E.6
  • 22
    • 3542998667 scopus 로고    scopus 로고
    • Nucleosomes facilitate their own invasion
    • Li G, Widom J. 2004. Nucleosomes facilitate their own invasion. Nature Structural & Molecular Biology 11:763–769. doi: 10.1038/nsmb801
    • (2004) Nature Structural & Molecular Biology , vol.11 , pp. 763-769
    • Li, G.1    Widom, J.2
  • 23
    • 0032504059 scopus 로고    scopus 로고
    • Activated rsc-nucleosome complex and persistently altered form of the nucleosome
    • Lorch Y, Cairns BR, Zhang M, Kornberg RD. 1998. Activated rsc-nucleosome complex and persistently altered form of the nucleosome. Cell 94:29–34. doi: 10.1016/S0092-8674(00)81218-0
    • (1998) Cell , vol.94 , pp. 29-34
    • Lorch, Y.1    Cairns, B.R.2    Zhang, M.3    Kornberg, R.D.4
  • 24
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology 276:19–42. doi: 10.1006/jmbi.1997.1494
    • (1998) Journal of Molecular Biology , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 25
    • 84862732690 scopus 로고    scopus 로고
    • New insights into nucleosome and chromatin structure: An ordered state or a disordered affair? Nature Reviews
    • Luger K, Dechassa ML, Tremethick DJ. 2012. New insights into nucleosome and chromatin structure: An ordered state or a disordered affair? Nature Reviews. Molecular Cell Biology 13:436–447. doi: 10.1038/nrm3382
    • (2012) Molecular Cell Biology , vol.13 , pp. 436-447
    • Luger, K.1    Dechassa, M.L.2    Tremethick, D.J.3
  • 26
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260. doi: 10.1038/38444
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mäder, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 27
    • 0033039285 scopus 로고    scopus 로고
    • Preparation of nucleosome core particle from recombinant histones
    • Luger K, Rechsteiner TJ, Richmond TJ. 1999. Preparation of nucleosome core particle from recombinant histones. B.-M. in Enzymology, 304:3–19. doi: 10.1016/S0076-6879(99)04003-3
    • (1999) B.-M. in Enzymology , vol.304 , pp. 3-19
    • Luger, K.1    Rechsteiner, T.J.2    Richmond, T.J.3
  • 28
    • 0033603212 scopus 로고    scopus 로고
    • Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer
    • Längst G, Bonte EJ, Corona DF, Becker PB. 1999. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97:843–852. doi: 10.1016/S0092-8674(00)80797-7
    • (1999) Cell , vol.97 , pp. 843-852
    • Längst, G.1    Bonte, E.J.2    Corona, D.F.3    Becker, P.B.4
  • 33
    • 0035691979 scopus 로고    scopus 로고
    • Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity
    • Narlikar GJ, Phelan ML, Kingston RE. 2001. Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Molecular Cell 8:1219–1230. doi: 10.1016/S1097-2765(01)00412-9
    • (2001) Molecular Cell , vol.8 , pp. 1219-1230
    • Narlikar, G.J.1    Phelan, M.L.2    Kingston, R.E.3
  • 34
    • 84881166117 scopus 로고    scopus 로고
    • Mechanisms and functions of atp-dependent chromatin-remodeling enzymes
    • Narlikar GJ, Sundaramoorthy R, Owen-Hughes T. 2013. Mechanisms and functions of atp-dependent chromatin-remodeling enzymes. Cell 154:490–503. doi: 10.1016/j.cell.2013.07.011
    • (2013) Cell , vol.154 , pp. 490-503
    • Narlikar, G.J.1    Sundaramoorthy, R.2    Owen-Hughes, T.3
  • 35
    • 0015964401 scopus 로고
    • Spheroid chromatin units (Ngr bodies)
    • Olins AL, Olins DE. 1974. Spheroid chromatin units (ngr bodies). Science 183:330–332. doi: 10.1126/science.183.4122.330
    • (1974) Science , vol.183 , pp. 330-332
    • Olins, A.L.1    Olins, D.E.2
  • 36
    • 67651101173 scopus 로고    scopus 로고
    • Chromatin remodelers act globally, sequence positions nucleosomes locally
    • Partensky PD, Narlikar GJ. 2009. Chromatin remodelers act globally, sequence positions nucleosomes locally. Journal of Molecular Biology 391:12. doi: 10.1016/j.jmb.2009.04.085
    • (2009) Journal of Molecular Biology , vol.391
    • Partensky, P.D.1    Narlikar, G.J.2
  • 37
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation
    • Polach KJ, Widom J. 1995. Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation. Journal of Molecular Biology 254:130–149. doi: 10.1006/jmbi.1995.0606
    • (1995) Journal of Molecular Biology , vol.254 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 38
    • 78149447722 scopus 로고    scopus 로고
    • The atp-dependent remodeler RSC transfers histone dimers and octamers through the rapid formation of an unstable encounter intermediate
    • Rowe CE, Narlikar GJ. 2010. The atp-dependent remodeler RSC transfers histone dimers and octamers through the rapid formation of an unstable encounter intermediate. Biochemistry 49:9882–9890. doi: 10.1021/bi101491u
    • (2010) Biochemistry , vol.49 , pp. 9882-9890
    • Rowe, C.E.1    Narlikar, G.J.2
  • 39
    • 84863205849 scopus 로고    scopus 로고
    • NIH image to imagej: 25 years of image analysis
    • Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH image to imagej: 25 years of image analysis. Nature Methods 9:671–675. doi: 10.1038/nmeth.2089
    • (2012) Nature Methods , vol.9 , pp. 671-675
    • Schneider, C.A.1    Rasband, W.S.2    Eliceiri, K.W.3
  • 40
    • 0032504102 scopus 로고    scopus 로고
    • Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state
    • Schnitzler G, Sif S, Kingston RE. 1998. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 94:17–27. doi: 10.1016/S0092-8674(00)81217-9
    • (1998) Cell , vol.94 , pp. 17-27
    • Schnitzler, G.1    Sif, S.2    Kingston, R.E.3
  • 42
    • 84946215320 scopus 로고    scopus 로고
    • Conformational control of DNA target cleavage by crispr–cas9
    • Sternberg SH, LaFrance B, Kaplan M, Doudna JA. 2015. Conformational control of DNA target cleavage by crispr–cas9. Nature 527:110–113. doi: 10.1038/nature15544
    • (2015) Nature , vol.527 , pp. 110-113
    • Sternberg, S.H.1    Lafrance, B.2    Kaplan, M.3    Doudna, J.A.4
  • 43
    • 84895871173 scopus 로고    scopus 로고
    • DNA interrogation by the CRISPR rna-guided endonuclease cas9
    • Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. 2014. DNA interrogation by the CRISPR rna-guided endonuclease cas9. Nature 507:62–67. doi: 10.1038/nature13011
    • (2014) Nature , vol.507 , pp. 62-67
    • Sternberg, S.H.1    Redding, S.2    Jinek, M.3    Greene, E.C.4    Doudna, J.A.5
  • 47
    • 84940726919 scopus 로고    scopus 로고
    • A candida albicans CRISPR system permits genetic engineering of essential genes and gene families
    • Vyas VK, Barrasa MI, Fink GR. 2015. A candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Science Advances 1. doi: 10.1126/sciadv.1500248
    • (2015) Science Advances
    • Vyas, V.K.1    Barrasa, M.I.2    Fink, G.R.3
  • 49
    • 84901611019 scopus 로고    scopus 로고
    • Genome-wide nucleosome positioning is orchestrated by genomic regions associated with dnase I hypersensitivity in rice
    • Wu Y, Zhang W, Jiang J. 2014. Genome-wide nucleosome positioning is orchestrated by genomic regions associated with dnase I hypersensitivity in rice. PLoS Genetics 10:e1004378. doi: 10.1371/journal.pgen.1004378
    • (2014) Plos Genetics , vol.10
    • Wu, Y.1    Zhang, W.2    Jiang, J.3
  • 50
    • 33845356072 scopus 로고    scopus 로고
    • The chromatin-remodeling enzyme ACF is an atp-dependent DNA length sensor that regulates nucleosome spacing
    • Yang JG, Madrid TS, Sevastopoulos E, Narlikar GJ. 2006. The chromatin-remodeling enzyme ACF is an atp-dependent DNA length sensor that regulates nucleosome spacing. Nature Structural & Molecular Biology 13: 1078–1083. doi: 10.1038/nsmb1170
    • (2006) Nature Structural & Molecular Biology , vol.13 , pp. 1078-1083
    • Yang, J.G.1    Madrid, T.S.2    Sevastopoulos, E.3    Narlikar, G.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.