메뉴 건너뛰기




Volumn 30, Issue 6, 2016, Pages 673-686

Integrated molecular mechanism directing nucleosome reorganization by human FACT

Author keywords

Chromatin remodeling; FACT; H2A H2B displacement; Histone chaperone; Nucleosome reorganization; Transcription

Indexed keywords

CHAPERONE; HISTONE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; PROTEIN FACILITATE CHROMATIN TRANSCRIPTION; PROTEIN SPT16; TETRAMER; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; AICDA (ACTIVATION-INDUCED CYTIDINE DEAMINASE); CYTIDINE DEAMINASE; DNA; DNA BINDING PROTEIN; HIGH MOBILITY GROUP PROTEIN; NUCLEOSOME; PROTEIN BINDING; SSRP1 PROTEIN, HUMAN; TRANSCRIPTION ELONGATION FACTOR;

EID: 84961187818     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.274183.115     Document Type: Article
Times cited : (117)

References (60)
  • 2
    • 84859893995 scopus 로고    scopus 로고
    • Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome
    • Arimura Y, Tachiwana H, Oda T, Sato M, Kurumizaka H. 2012. Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome. Biochemistry 51: 3302–3309.
    • (2012) Biochemistry , vol.51 , pp. 3302-3309
    • Arimura, Y.1    Tachiwana, H.2    Oda, T.3    Sato, M.4    Kurumizaka, H.5
  • 3
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98: 10037–10041.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 4
    • 84902168468 scopus 로고    scopus 로고
    • Regulating the chromatin landscape: Structural and mechanistic perspectives
    • Bartholomew B. 2014. Regulating the chromatin landscape: structural and mechanistic perspectives. Annu Rev Biochem 83: 671–696.
    • (2014) Annu Rev Biochem , vol.83 , pp. 671-696
    • Bartholomew, B.1
  • 6
    • 84933514672 scopus 로고    scopus 로고
    • Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2
    • Chen S, Rufiange A, Huang H, Rajashankar KR, Nourani A, Patel DJ. 2015. Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. Genes Dev 29: 1326–1340.
    • (2015) Genes Dev , vol.29 , pp. 1326-1340
    • Chen, S.1    Rufiange, A.2    Huang, H.3    Rajashankar, K.R.4    Nourani, A.5    Patel, D.J.6
  • 7
    • 84864487717 scopus 로고    scopus 로고
    • The mechanics behindDNAsequence-dependent properties of the nucleosome
    • Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA. 2012. The mechanics behindDNAsequence-dependent properties of the nucleosome. Nucleic Acids Res 40: 6338–6352.
    • (2012) Nucleic Acids Res , vol.40 , pp. 6338-6352
    • Chua, E.1    Vasudevan, D.2    Davey, G.E.3    Wu, B.4    Davey, C.A.5
  • 10
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P, Cowtan K. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 13
    • 0036964090 scopus 로고    scopus 로고
    • Defects in SPT16 or POB3 (YFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: Polymerase passage may degrade chromatin structure
    • Formosa T, Ruone S, Adams M, Olsen A, Eriksson P, Yu Y, Rhoades AR, Kaufman P, Stillman DJ. 2002. Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure. Genetics 162: 1557–1571.
    • (2002) Genetics , vol.162 , pp. 1557-1571
    • Formosa, T.1    Ruone, S.2    Adams, M.3    Olsen, A.4    Eriksson, P.5    Yu, Y.6    Rhoades, A.R.7    Kaufman, P.8    Stillman, D.J.9
  • 14
    • 84902203517 scopus 로고    scopus 로고
    • Histone chaperones: Assisting histone traffic and nucleosome dynamics
    • Gurard-Levin ZA, Quivy J-P, Almouzni G. 2014. Histone chaperones: assisting histone traffic and nucleosome dynamics. Annu Rev Biochem 83: 487–517.
    • (2014) Annu Rev Biochem , vol.83 , pp. 487-517
    • Gurard-Levin, Z.A.1    Quivy, J.-P.2    Almouzni, G.3
  • 15
    • 84876211475 scopus 로고    scopus 로고
    • Identification of mutant versions of the Spt16 histone chaperone that are defective for transcription-coupled nucleosome occupancy in Saccharomyces cerevisiae
    • Hainer SJ, Charsar BA, Cohen SB, Martens JA. 2012. Identification of mutant versions of the Spt16 histone chaperone that are defective for transcription-coupled nucleosome occupancy in Saccharomyces cerevisiae. G3 (Bethesda) 2: 555–567.
    • (2012) G3 (Bethesda) , vol.2 , pp. 555-567
    • Hainer, S.J.1    Charsar, B.A.2    Cohen, S.B.3    Martens, J.A.4
  • 17
    • 84878138537 scopus 로고    scopus 로고
    • Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT
    • Hashimoto M, Kodera N, Tsunaka Y, Oda M, Tanimoto M, Ando T, Morikawa K, Tate S-I. 2013. Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT. Biophys J 104: 2222–2234.
    • (2013) Biophys J , vol.104 , pp. 2222-2234
    • Hashimoto, M.1    Kodera, N.2    Tsunaka, Y.3    Oda, M.4    Tanimoto, M.5    O, T.6    Morikawa, K.7    Tate, S.-I.8
  • 18
    • 41549112501 scopus 로고    scopus 로고
    • FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16
    • Heo K, Kim H, Choi S, Choi J, Kim K, Gu J, Lieber M, Yang A, An W. 2008. FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16. Mol Cell 30: 86–97.
    • (2008) Mol Cell , vol.30 , pp. 86-97
    • Heo, K.1    Kim, H.2    Choi, S.3    Choi, J.4    Kim, K.5    Gu, J.6    Lieber, M.7    Yang, A.8    An, W.9
  • 23
    • 84876275605 scopus 로고    scopus 로고
    • Structure of the Spt16 middle domain reveals functional features of the histone chaperone FACT
    • Kemble DJ, Whitby FG, Robinson H, McCullough L, Formosa T, Hill CP. 2013. Structure of the Spt16 middle domain reveals functional features of the histone chaperone FACT. J Biol Chem 288: 10188–10194.
    • (2013) J Biol Chem , vol.288 , pp. 10188-10194
    • Kemble, D.J.1    Whitby, F.G.2    Robinson, H.3    McCullough, L.4    Formosa, T.5    Hill, C.P.6
  • 24
    • 84944873198 scopus 로고    scopus 로고
    • FACT disrupts nucleosome structure by binding H2A–H2B with conserved peptide motifs
    • Kemble DJ, McCullough L, Whitby FG, Formosa T, Hill CP. 2015. FACT disrupts nucleosome structure by binding H2A–H2B with conserved peptide motifs. Mol Cell 60: 294–306.
    • (2015) Mol Cell , vol.60 , pp. 294-306
    • Kemble, D.J.1    McCullough, L.2    Whitby, F.G.3    Formosa, T.4    Hill, C.P.5
  • 26
    • 84887161037 scopus 로고    scopus 로고
    • Control of transcriptional elongation
    • Kwak H, Lis JT. 2013. Control of transcriptional elongation. Annu Rev Genet 47: 483–508.
    • (2013) Annu Rev Genet , vol.47 , pp. 483-508
    • Kwak, H.1    Lis, J.T.2
  • 27
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu LF, Wang JC. 1987. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci 84: 7024.
    • (1987) Proc Natl Acad Sci , vol.84 , pp. 7024
    • Liu, L.F.1    Wang, J.C.2
  • 29
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • Lowary P, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19–42.
    • (1998) J Mol Biol , vol.276 , pp. 19-42
    • Lowary, P.1    Widom, J.2
  • 30
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger K, Mader A, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal 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.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 31
    • 84883732664 scopus 로고    scopus 로고
    • Nucleosome sliding mechanisms: New twists in a looped history
    • Mueller-Planitz F, Klinker H, Becker PB. 2013. Nucleosome sliding mechanisms: new twists in a looped history. Nat Struct Mol Biol 20: 1026–1032.
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 1026-1032
    • Mueller-Planitz, F.1    Klinker, H.2    Becker, P.B.3
  • 32
    • 79958078987 scopus 로고    scopus 로고
    • Mutant versions of the S. Cerevisiae transcription elongation factor Spt16 define regions of Spt16 that functionally interact with histone H3
    • Myers CN, Berner GB, Holthoff JH, Martinez-Fonts K, Harper JA, Alford S, Taylor MN, Duina AA. 2011. Mutant versions of the S. cerevisiae transcription elongation factor Spt16 define regions of Spt16 that functionally interact with histone H3. PLoS One 6: e20847.
    • (2011) Plos One , vol.6
    • Myers, C.N.1    Berner, G.B.2    Holthoff, J.H.3    Martinez-Fonts, K.4    Harper, J.A.5    Alford, S.6    Taylor, M.N.7    Duina, A.A.8
  • 33
    • 77950513764 scopus 로고    scopus 로고
    • A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNArepair and Swi/Snf binding in UV irradiated yeast
    • Nag R, Kyriss M, Smerdon JW, Wyrick JJ, Smerdon MJ. 2010. A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNArepair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Res 38: 1450–1460.
    • (2010) Nucleic Acids Res , vol.38 , pp. 1450-1460
    • Nag, R.1    Kyriss, M.2    Smerdon, J.W.3    Wyrick, J.J.4    Smerdon, M.J.5
  • 34
    • 33947138617 scopus 로고    scopus 로고
    • Drosophila GAGA factor directs histone H3.3 replacement that prevents the heterochromatin spreading
    • Nakayama T, Nishioka K, Dong Y-X, Shimojima T, Hirose S. 2007. Drosophila GAGA factor directs histone H3.3 replacement that prevents the heterochromatin spreading. Genes Dev 21: 552–561.
    • (2007) Genes Dev , vol.21 , pp. 552-561
    • Nakayama, T.1    Nishioka, K.2    Dong, Y.-X.3    Shimojima, T.4    Hirose, S.5
  • 35
    • 84870028442 scopus 로고    scopus 로고
    • The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions
    • Nakayama T, Shimojima T, Hirose S. 2012. The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions. Development 139: 4582–4590.
    • (2012) Development , vol.139 , pp. 4582-4590
    • Nakayama, T.1    Shimojima, T.2    Hirose, S.3
  • 36
    • 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.
    • (2013) Cell , vol.154 , pp. 490-503
    • Narlikar, G.J.1    Sundaramoorthy, R.2    Owen-Hughes, T.3
  • 37
    • 33847226680 scopus 로고    scopus 로고
    • Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4
    • Natsume R, Eitoku M, Akai Y, Sano N, Horikoshi M, Senda T. 2007. Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4. Nature 446: 338–341.
    • (2007) Nature , vol.446 , pp. 338-341
    • Natsume, R.1    Eitoku, M.2    Akai, Y.3    Sano, N.4    Horikoshi, M.5    Senda, T.6
  • 38
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307–326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 39
    • 33646580356 scopus 로고    scopus 로고
    • Deciphering the roles of the histone H2B N-terminal domain in genome- wide transcription
    • Parra MA, Kerr D, Fahy D, Pouchnik DJ, Wyrick JJ. 2006. Deciphering the roles of the histone H2B N-terminal domain in genome- wide transcription. Mol Cell Biol 26: 3842–3852.
    • (2006) Mol Cell Biol , vol.26 , pp. 3842-3852
    • Parra, M.A.1    Kerr, D.2    Fahy, D.3    Pouchnik, D.J.4    Wyrick, J.J.5
  • 41
    • 74549138158 scopus 로고    scopus 로고
    • Chaperoning histones during DNA replication and repair
    • Ransom M, Dennehey BK, Tyler JK. 2010. Chaperoning histones during DNA replication and repair. Cell 140: 183–195.
    • (2010) Cell , vol.140 , pp. 183-195
    • Ransom, M.1    Dennehey, B.K.2    Tyler, J.K.3
  • 42
    • 84923596623 scopus 로고    scopus 로고
    • Subnucleosomal structures and nucleosome asymmetry across a genome
    • Rhee HS, Bataille AR, Zhang L, Pugh BF. 2014. Subnucleosomal structures and nucleosome asymmetry across a genome. Cell 159: 1377–1388.
    • (2014) Cell , vol.159 , pp. 1377-1388
    • Rhee, H.S.1    Bataille, A.R.2    Zhang, L.3    Pugh, B.F.4
  • 44
    • 84885660614 scopus 로고    scopus 로고
    • Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
    • Sheinin MY, Li M, Soltani M, Luger K, Wang MD. 2013. Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun 4: 2579.
    • (2013) Nat Commun , vol.4 , pp. 2579
    • Sheinin, M.Y.1    Li, M.2    Soltani, M.3    Luger, K.4    Wang, M.D.5
  • 46
    • 0037423733 scopus 로고    scopus 로고
    • Sequence-dependent nucleosome structural and dynamic polymorphism. Potential involvement of histone H2B N-terminal tail proximal domain
    • Sivolob A, Lavelle C, Prunell A. 2003. Sequence-dependent nucleosome structural and dynamic polymorphism. Potential involvement of histone H2B N-terminal tail proximal domain. J Mol Biol 326: 49–63.
    • (2003) J Mol Biol , vol.326 , pp. 49-63
    • Sivolob, A.1    Lavelle, C.2    Prunell, A.3
  • 47
    • 79959484677 scopus 로고    scopus 로고
    • Signals and combinatorial functions of histone modifications
    • Suganuma T, Workman JL. 2011. Signals and combinatorial functions of histone modifications. Annu Rev Biochem 80: 473–499.
    • (2011) Annu Rev Biochem , vol.80 , pp. 473-499
    • Suganuma, T.1    Workman, J.L.2
  • 48
    • 65649153311 scopus 로고    scopus 로고
    • FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter
    • Takahata S, Yu Y, Stillman DJ. 2009. FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Mol Cell 34: 405–415.
    • (2009) Mol Cell , vol.34 , pp. 405-415
    • Takahata, S.1    Yu, Y.2    Stillman, D.J.3
  • 49
    • 33748357745 scopus 로고    scopus 로고
    • Functional cooperation between FACT and MCM helicase facilitates initiation of chromatin DNA replication
    • Tan BC-M, Chien C-T, Hirose S, Lee S-C. 2006. Functional cooperation between FACT and MCM helicase facilitates initiation of chromatin DNA replication. EMBO J 25: 3975–3985.
    • (2006) EMBO J , vol.25 , pp. 3975-3985
    • Tan, B.-M.1    Chien, C.-T.2    Hirose, S.3    Lee, S.-C.4
  • 50
    • 84893755427 scopus 로고    scopus 로고
    • Transcription-generated torsional stress destabilizes nucleosomes
    • Teves SS, Henikoff S. 2014. Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol 21: 88–94.
    • (2014) Nat Struct Mol Biol , vol.21 , pp. 88-94
    • Teves, S.S.1    Henikoff, S.2
  • 51
    • 33847106524 scopus 로고    scopus 로고
    • Higher-order structures of chromatin: The elusive 30 nm fiber
    • Tremethick DJ. 2007. Higher-order structures of chromatin: the elusive 30 nm fiber. Cell 128: 651–654.
    • (2007) Cell , vol.128 , pp. 651-654
    • Tremethick, D.J.1
  • 52
    • 20444462007 scopus 로고    scopus 로고
    • Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle
    • Tsunaka Y, Kajimura N, Tate S, Morikawa K. 2005. Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucleic Acids Res 33: 3424–3434.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3424-3434
    • Tsunaka, Y.1    Kajimura, N.2    Tate, S.3    Morikawa, K.4
  • 53
    • 69949134806 scopus 로고    scopus 로고
    • Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements
    • Tsunaka Y, Toga J, Yamaguchi H, Tate S-I, Hirose S, Morikawa K. 2009. Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements. J Biol Chem 284: 24610–24621.
    • (2009) J Biol Chem , vol.284 , pp. 24610-24621
    • Tsunaka, Y.1    Toga, J.2    Yamaguchi, H.3    Tate, S.-I.4    Hirose, S.5    Morikawa, K.6
  • 54
    • 33646153980 scopus 로고    scopus 로고
    • The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition
    • VanDemark A, Blanksma M, Ferris E, Heroux A, Hill CP, Formosa T. 2006. The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol Cell 22: 363–374.
    • (2006) Mol Cell , vol.22 , pp. 363-374
    • Vandemark, A.1    Blanksma, M.2    Ferris, E.3    Heroux, A.4    Hill, C.P.5    Formosa, T.6
  • 56
    • 82355184456 scopus 로고    scopus 로고
    • Histone chaperone FACTcoordinates nucleosome interaction through multiple synergistic binding events
    • Winkler DD, Muthurajan UM, Hieb AR, Luger K. 2011. Histone chaperone FACTcoordinates nucleosome interaction through multiple synergistic binding events. J Biol Chem 286: 41883–41892.
    • (2011) J Biol Chem , vol.286 , pp. 41883-41892
    • Winkler, D.D.1    Muthurajan, U.M.2    Hieb, A.R.3    Luger, K.4
  • 59
    • 68349131435 scopus 로고    scopus 로고
    • YFACTinduces global accessibility of nucleosomal DNA without H2A–H2B displacement
    • Xin H, Takahata S, Blanksma M, McCullough L, Stillman DJ, Formosa T. 2009. yFACTinduces global accessibility of nucleosomal DNA without H2A–H2B displacement. Mol Cell 35: 365–376.
    • (2009) Mol Cell , vol.35 , pp. 365-376
    • Xin, H.1    Takahata, S.2    Blanksma, M.3    McCullough, L.4    Stillman, D.J.5    Formosa, T.6
  • 60
    • 84892458543 scopus 로고    scopus 로고
    • A highly conserved region within H2B is important for FACT to act on nucleosomes
    • Zheng S, Crickard JB, Srikanth A, Reese JC. 2014. A highly conserved region within H2B is important for FACT to act on nucleosomes. Mol Cell Biol 34: 303–314.
    • (2014) Mol Cell Biol , vol.34 , pp. 303-314
    • Zheng, S.1    Crickard, J.B.2    Srikanth, A.3    Reese, J.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.