Dynamics and function of compact nucleosome arrays.
The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg2+-dependent folding similar to that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on timescales in the second to microsecond range. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allow for the invasion and action of DNA-processing protein complexes.
Poirier
Michael G
MG
Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois, USA.
Oh
Eugene
E
Tims
Hannah S
HS
Widom
Jonathan
J
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D009707:Nucleosomes / Q000737:chemistry*; D011485:Protein Binding; D012697:Serine Endopeptidases / Q000235:genetics / Q000378:metabolism; D000099160:LexA Repressor Protein
D001426:Bacterial Proteins; D009707:Nucleosomes; D012697:Serine Endopeptidases; D000099160:LexA Repressor Protein
Methods Enzymol. 1992;211:353-88
1406315
Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11176-81
18676615
Cell. 2005 Dec 29;123(7):1199-212
16377562
Biochemistry. 1993 Aug 3;32(30):7824-31
8347588
Annu Rev Biophys Bioeng. 1975;4(00):311-34
1098559
J Mol Biol. 2004 May 7;338(4):695-709
15099738
Mol Cell Biol. 1995 Mar;15(3):1405-21
7862134
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8872-7
18583476
J Mol Biol. 2008 Jun 13;379(4):772-86
18485363
Proc Natl Acad Sci U S A. 1990 Oct;87(19):7603-7
2217191
Nature. 2007 May 24;447(7143):399-406
17522672
Biochemistry. 2006 Sep 12;45(36):10838-46
16953569
J Cell Biol. 2005 Jan 3;168(1):41-54
15623580
Yeast. 1997 Feb;13(2):151-61
9046096
J Mol Biol. 2006 Aug 25;361(4):617-24
16860337
Cell. 2005 Jan 14;120(1):37-48
15652480
Methods. 2004 May;33(1):33-44
15039085
Mol Cell Biol. 2003 Mar;23(5):1623-32
12588982
Methods Enzymol. 1994;244:266-84
7845214
J Mol Biol. 2000 Mar 3;296(4):979-87
10686097
Curr Opin Struct Biol. 2005 Apr;15(2):188-96
15837178
Genome Biol. 2004;5(9):R62
15345046
Nat Struct Mol Biol. 2005 Jan;12(1):46-53
15580276
Nucleic Acids Res. 1981 Nov 25;9(22):5883-94
7312631
J Mol Biol. 1996 May 24;258(5):800-12
8637011
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8602-6
9671724
Biochemistry. 2002 Jan 22;41(3):697-705
11790090
Science. 2004 Nov 26;306(5701):1571-3
15567867
EMBO J. 2006 Jul 12;25(13):3123-32
16778764
Genome Res. 2008 Jul;18(7):1084-91
18448704
Curr Biol. 1998 Nov 5;8(22):R788-91
9811600
Nat Struct Mol Biol. 2004 Aug;11(8):763-9
15258568
J Mol Biol. 1998 Feb 13;276(1):19-42
9514715
Nature. 2003 May 8;423(6936):145-50
12736678
Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5397-402
15809441
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6506-11
16617109
J Mol Biol. 2003 Mar 14;327(1):85-96
12614610
Annu Rev Genet. 1980;14:121-44
6260016
Nature. 2005 Jul 7;436(7047):138-41
16001076
J Mol Biol. 1995 Nov 24;254(2):130-49
7490738
Methods Enzymol. 1999;304:278-98
10372366
Annu Rev Biophys Biophys Chem. 1989;18:365-95
2660830
Nat Struct Mol Biol. 2007 Nov;14(11):1041-8
17984966
Biochem Biophys Res Commun. 1998 Jun 18;247(2):530-5
9642164
Science. 2006 Feb 10;311(5762):844-7
16469925
Curr Opin Plant Biol. 2006 Dec;9(6):647-53
17015032
Curr Opin Struct Biol. 2006 Jun;16(3):336-43
16714106
Science. 2003 Jan 31;299(5607):721-5
12560555
Mol Cell Biol. 2002 Oct;22(20):7147-57
12242292
DNA Repair (Amst). 2005 Jul 28;4(8):919-25
15961352