title: Human CAF-1-dependent nucleosome assembly in a defined system.
abstract: Replication-coupled nucleosome assembly is a critical step in packaging newly synthesized DNA into chromatin. Previous studies have defined the importance of the histone chaperones CAF-1 and ASF1A, the replicative clamp PCNA, and the clamp loader RFC for the assembly of nucleosomes during DNA replication. Despite significant progress in the field, replication-coupled nucleosome assembly is not well understood. One of the complications in elucidating the mechanisms of replication-coupled nucleosome assembly is the lack of a defined system that faithfully recapitulates this important biological process in vitro. We describe here a defined system that assembles nucleosomal arrays in a manner dependent on the presence of CAF-1, ASF1A-H3-H4, H2A-H2B, PCNA, RFC, NAP1L1, ATP, and strand breaks. The loss of CAF-1 p48 subunit causes a strong defect in packaging DNA into nucleosomes by this system. We also show that the defined system forms nucleosomes on nascent DNA synthesized by the replicative polymerase δ. Thus, the developed system reproduces several key features of replication-coupled nucleosome assembly.
authors.affiliation: Department of Biochemistry and Molecular Biology; Southern Illinois University School of Medicine; Carbondale, IL USA.
authors.forename: Lyudmila Y
authors.initials: LY
authors.lastname: Kadyrova
authors.forename: Elena
authors.initials: E
authors.lastname: Rodriges Blanko
authors.forename: Farid A
authors.initials: FA
authors.lastname: Kadyrov
mesh_terms: D018797:Cell Cycle Proteins / Q000302:isolation & purification / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D003600:Cytosol / Q000378:metabolism; D004247:DNA / Q000235:genetics; D042003:DNA Packaging; D006367:HeLa Cells; D006657:Histones / Q000302:isolation & purification / Q000378:metabolism; D006801:Humans; D018832:Molecular Chaperones; D009707:Nucleosomes / Q000378:metabolism*; D011994:Recombinant Proteins / Q000302:isolation & purification; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: C491641:ASF1A protein, human; C489780:CNOT8 protein, human; D018797:Cell Cycle Proteins; D006657:Histones; D018832:Molecular Chaperones; D009707:Nucleosomes; D011994:Recombinant Proteins; D014157:Transcription Factors; D004247:DNA
keywords: ASF1; CAF-1; DNA polymerase delta; PCNA; RFC; chromatin; histone chaperone; nucleosome assembly; replication
references.citation: Cell. 2006 Jul 28;126(2):297-308
references.pmid: 16873062
references.citation: Mol Cell. 2008 Apr 25;30(2):137-44
references.pmid: 18439893
references.citation: Cell. 1986 May 23;45(4):555-65
references.pmid: 3011272
references.citation: Biochim Biophys Acta. 2008 Sep;1783(9):1595-604
references.pmid: 18474252
references.citation: Science. 2007 Dec 21;318(5858):1928-31
references.pmid: 18096807
references.citation: DNA. 1985 Apr;4(2):157-64
references.pmid: 3996184
references.citation: Mol Cell Biol. 2000 Feb;20(4):1206-18
references.pmid: 10648606
references.citation: Mol Cell. 2004 Jul 2;15(1):31-41
references.pmid: 15225546
references.citation: Proc Natl Acad Sci U S A. 2009 May 26;106(21):8495-500
references.pmid: 19420220
references.citation: Genetics. 2000 Aug;155(4):1593-606
references.pmid: 10924459
references.citation: Cell. 1989 Jul 14;58(1):15-25
references.pmid: 2546672
references.citation: EMBO J. 1991 Apr;10(4):971-80
references.pmid: 1849080
references.citation: Nature. 1999 Dec 2;402(6761):555-60
references.pmid: 10591219
references.citation: Trends Genet. 2004 Jul;20(7):320-6
references.pmid: 15219397
references.citation: Cell. 2004 Jan 9;116(1):51-61
references.pmid: 14718166
references.citation: Nat Struct Mol Biol. 2009 Nov;16(11):1167-72
references.pmid: 19855395
references.citation: Mol Cell Biol. 1996 Jun;16(6):3112-24
references.pmid: 8649423
references.citation: Biochemistry. 2005 Oct 25;44(42):13673-82
references.pmid: 16229457
references.citation: Nature. 1977 Mar 17;266(5599):273-5
references.pmid: 846573
references.citation: Nature. 1994 May 19;369(6477):207-12
references.pmid: 7910375
references.citation: J Biol Chem. 1994 Apr 8;269(14):10923-34
references.pmid: 8144677
references.citation: Nat Struct Mol Biol. 2013 Jan;20(1):14-22
references.pmid: 23288364
references.citation: Cell. 1999 Feb 19;96(4):575-85
references.pmid: 10052459
references.citation: Nat Struct Mol Biol. 2008 May;15(5):477-84
references.pmid: 18408730
references.citation: Mol Cell Biol. 2002 Jan;22(2):614-25
references.pmid: 11756556
references.citation: Genes Dev. 1997 Feb 1;11(3):345-57
references.pmid: 9030687
references.citation: J Biol Chem. 2002 Feb 8;277(6):3894-901
references.pmid: 11711545
references.citation: Curr Biol. 2005 Nov 22;15(22):2044-9
references.pmid: 16303565
references.citation: Mol Cell. 2011 Aug 19;43(4):638-48
references.pmid: 21855802
references.citation: Mol Cell Biol. 1989 Feb;9(2):609-19
references.pmid: 2565531
references.citation: FASEB J. 2006 Mar;20(3):488-90
references.pmid: 16396992
references.citation: Proc Natl Acad Sci U S A. 1990 Feb;87(3):1023-7
references.pmid: 1967833
references.citation: J Biol Chem. 1991 Jan 25;266(3):1950-60
references.pmid: 1671045
references.citation: Protein Expr Purif. 2010 Aug;72(2):194-204
references.pmid: 20347990
references.citation: Genes Dev. 2004 Nov 15;18(22):2764-73
references.pmid: 15520275
references.citation: Nucleic Acids Res. 2012 Dec;40(22):11229-39
references.pmid: 23034810
references.citation: Curr Biol. 2003 Dec 16;13(24):2148-58
references.pmid: 14680630
references.citation: FEBS Lett. 2008 Jun 18;582(14):1938-49
references.pmid: 18343227
references.citation: J Biol Chem. 2009 Feb 13;284(7):4041-5
references.pmid: 18835809
references.citation: Cell. 1995 Jun 30;81(7):1105-14
references.pmid: 7600578
references.citation: Mol Cell Biol. 2009 Dec;29(24):6353-65
references.pmid: 19822659
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2753-8
references.pmid: 21282622
references.citation: Science. 2003 Aug 22;301(5636):1090-3
references.pmid: 12934006
references.citation: Histopathology. 2010 Nov;57(5):716-24
references.pmid: 21083601
references.citation: Mol Cell. 2005 Jan 21;17(2):301-11
references.pmid: 15664198
references.citation: Nucleic Acids Res. 2008 Apr;36(7):2208-18
references.pmid: 18281699
references.citation: Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7766-71
references.pmid: 10884407
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1525-30
references.pmid: 14732680
references.citation: Cell. 2010 Jan 22;140(2):183-95
references.pmid: 20141833
references.citation: Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16066-71
references.pmid: 20713735
references.citation: Nucleic Acids Res. 2012 Nov 1;40(20):10139-49
references.pmid: 22941638
references.citation: Nature. 2012 Mar 14;483(7390):434-8
references.pmid: 22419157
references.citation: Nat Genet. 2002 Dec;32(4):627-32
references.pmid: 12434153
references.citation: Cell. 2007 Feb 23;128(4):721-33
references.pmid: 17320509
references.citation: Proc Natl Acad Sci U S A. 2003 May 27;100(11):6640-5
references.pmid: 12750463
references.citation: Mol Cell Biol. 2004 Apr;24(7):2853-62
references.pmid: 15024074
references.citation: Mol Cell Biol. 1985 Nov;5(11):2879-86
references.pmid: 3018484
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Cell. 2006 Nov 3;127(3):495-508
references.pmid: 17081973
references.citation: Curr Biol. 2001 Jul 10;11(13):1068-73
references.pmid: 11470414
references.citation: Mol Cell. 2010 Mar 26;37(6):834-42
references.pmid: 20347425
references.citation: Nature. 1987 Apr 2-8;326(6112):517-20
references.pmid: 2882424
references.citation: EMBO J. 2001 Dec 17;20(24):7294-302
references.pmid: 11743005
references.citation: J Mol Biol. 2011 Apr 15;407(5):647-60
references.pmid: 21333655
references.citation: EMBO J. 2011 Feb 2;30(3):480-93
references.pmid: 21179005
references.citation: Nature. 2007 Mar 15;446(7133):338-41
references.pmid: 17293877
references.citation: EMBO Rep. 2002 Apr;3(4):329-34
references.pmid: 11897662
references.citation: Cell. 1996 Oct 4;87(1):95-104
references.pmid: 8858152
references.citation: Science. 1974 May 24;184(4139):868-71
references.pmid: 4825889
references.citation: Cell. 2007 May 18;129(4):665-79
references.pmid: 17512402
references.citation: J Biol Chem. 2006 May 12;281(19):13817-13827
references.pmid: 16537536
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12183-8
references.pmid: 14519857
references.citation: J Mol Biol. 1986 May 5;189(1):189-204
references.pmid: 3023620