Chromatin higher-order structure and dynamics.
The primary role of the nucleus as an information storage, retrieval, and replication site requires the physical organization and compaction of meters of DNA. Although it has been clear for many years that nucleosomes constitute the first level of chromatin compaction, this contributes a relatively small fraction of the condensation needed to fit the typical genome into an interphase nucleus or set of metaphase chromosomes, indicating that there are additional "higher order" levels of chromatin condensation. Identifying these levels, their interrelationships, and the principles that govern their occurrence has been a challenging and much discussed problem. In this article, we focus on recent experimental advances and the emerging evidence indicating that structural plasticity and chromatin dynamics play dominant roles in genome organization. We also discuss novel approaches likely to yield important insights in the near future, and suggest research areas that merit further study.
Woodcock
Christopher L
CL
Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA. chris@bio.umass.edu
Ghosh
Rajarshi P
RP
D002467:Cell Nucleus / Q000737:chemistry; D002843:Chromatin / Q000737:chemistry* / Q000502:physiology*; D003198:Computer Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
D002843:Chromatin
J Cell Biol. 2004 Sep 13;166(6):775-85
15353545
Science. 2002 Mar 15;295(5562):2080-3
11859155
Science. 2002 Apr 5;296(5565):158-62
11935030
Biol Cell. 2004 Oct;96(8):595-601
15519694
Cell. 2007 Feb 23;128(4):651-4
17320503
Mol Cell. 2007 Oct 12;28(1):1-13
17936700
Cell. 2007 Feb 23;128(4):693-705
17320507
Curr Biol. 2002 Mar 19;12(6):439-45
11909528
Science. 2009 Oct 9;326(5950):289-93
19815776
Nature. 2000 Apr 6;404(6778):604-9
10766243
Hum Genet. 1982;60(1):46-56
7076247
Nat Methods. 2008 Apr;5(4):311-3
18345005
J Cell Biol. 1981 Dec;91(3 Pt 2):3s-14s
7033242
Exp Cell Res. 1999 Nov 1;252(2):363-75
10527626
J Cell Biol. 1983 Jan;96(1):84-93
6826654
J Cell Biol. 1996 Nov;135(3):545-57
8909532
J Mol Biol. 1986 Apr 20;188(4):613-29
3016287
Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20222-7
19923429
J Cell Sci. 1975 Nov;19(2):261-79
1202042
Nat Methods. 2007 Mar;4(3):215-7
17277781
Cell Cycle. 2006 Mar;5(6):589-91
16582611
Biochim Biophys Acta. 2009 Jan;1789(1):17-25
18675948
J Biol Chem. 1995 Apr 14;270(15):8373-6
7721727
Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13317-22
19651606
Science. 2001 Aug 10;293(5532):1074-80
11498575
Cell. 2009 Apr 17;137(2):356-68
19379699
Cold Spring Harb Symp Quant Biol. 2006;71:461-71
17381328
Science. 1986 Nov 14;234(4778):863-6
3775367
Curr Top Dev Biol. 2003;55:75-141
12959194
Mol Cell. 2004 Nov 19;16(4):655-61
15546624
Nat Rev Mol Cell Biol. 2004 May;5(5):367-78
15122350
Chromosome Res. 2008;16(3):469-97
18461485
Curr Opin Cell Biol. 2007 Jun;19(3):326-30
17467255
Biochemistry. 2000 Apr 11;39(14):3861-6
10747773
Biochimie. 2008 Jul;90(7):1040-51
18331845
Chromosoma. 2007 Aug;116(4):349-72
17333236
Methods Cell Biol. 1999;58:203-22
9891383
Chromosoma. 2000 Jun;109(3):181-9
10929196
J Cell Biol. 2001 Jul 9;154(1):33-48
11448988
Mol Cell Biol. 2003 Jul;23(13):4559-72
12808097
Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):127-32
10618382
Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16236-41
17060627
Science. 1983 May 13;220(4598):719-21
6601299
Trends Cell Biol. 1995 Jul;5(7):272-7
14732111
J Cell Sci. 2000 May;113 ( Pt 9):1565-76
10751148
Semin Cell Dev Biol. 2007 Oct;18(5):651-8
17905614
Trends Cell Biol. 1998 May;8(5):207
9695841
Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15393-7
12438695
Chromosoma. 1989 Aug;98(2):129-43
2476279
Annu Rev Biophys. 2010;39:471-89
20462379
Mol Cell. 2009 Apr 24;34(2):155-67
19394293
Nat Struct Mol Biol. 2009 May;16(5):534-40
19377481
Development. 2005 May;132(9):2215-23
15829525
Curr Biol. 2006 Apr 18;16(8):825-31
16631592
Curr Opin Cell Biol. 2006 Dec;18(6):632-8
17046228
Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):525-30
17194760
J Cell Biol. 1994 Oct;127(2):287-302
7929576
Nat Struct Biol. 2000 Dec;7(12):1121-4
11101893
Annu Rev Biochem. 2009;78:273-304
19355820
Science. 2009 Nov 27;326(5957):1230
19933109
Nat Rev Genet. 2003 Jul;4(7):520-34
12838344
Cell. 1985 Oct;42(3):799-808
2996776
Curr Opin Struct Biol. 2005 Apr;15(2):188-96
15837178
Mol Biol Cell. 2000 Mar;11(3):799-805
10712500
Nature. 2009 Sep 10;461(7261):199-205
19741700
J Cell Biol. 2001 Dec 10;155(6):899-910
11739403
Prog Nucleic Acid Res Mol Biol. 1991;40:143-84
2031082
Curr Biol. 2002 Mar 5;12(5):R185-92
11882311
Mol Cell Biol. 2004 Nov;24(21):9359-70
15485905
Nature. 2008 Sep 25;455(7212):557-60
18716622
Nature. 2009 Aug 13;460(7257):863-8
19587682
Nat Cell Biol. 2006 Oct;8(10):1133-42
16998479
Cell. 1997 Dec 12;91(6):845-54
9413993
Genes Dev. 2000 Apr 15;14(8):940-50
10783166
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2824-9
11880634
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8872-7
18583476
Biochim Biophys Acta. 2008 Nov;1783(11):2100-7
18723053
Biophys J. 2005 Dec;89(6):4275-85
16150965
Curr Opin Genet Dev. 2007 Oct;17(5):435-42
17905579
Science. 2002 May 24;296(5572):1412-6
12029120
Cell Cycle. 2006 Sep;5(17):1910-2
16929171
J Mol Biol. 1990 Feb 20;211(4):883-96
2313700
EMBO J. 2009 Dec 16;28(24):3785-98
19927119
Mol Cell Biol. 2006 Oct;26(20):7616-31
16908543
Curr Opin Genet Dev. 2001 Apr;11(2):130-5
11250134
J Struct Biol. 2004 Jun;146(3):281-90
15099570
J Cell Biol. 1999 Jun 28;145(7):1341-54
10385516
Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14173-8
9826673
Nat Rev Mol Cell Biol. 2006 May;7(5):311-22
16633335
Science. 2004 Jan 30;303(5658):672-6
14704433
Genetics. 2009 Aug;182(4):967-77
19487560
J Cell Biol. 1997 Oct 6;139(1):1-12
9314524
J Cell Biol. 2006 Jul 3;174(1):27-38
16818717
J Biol Chem. 2001 Apr 6;276(14):10577-80
11279227
J Cell Biol. 1993 Feb;120(3):601-12
8381118
Science. 2004 Nov 26;306(5701):1571-3
15567867
J Cell Biol. 1994 Apr;125(1):1-10
8138564
Nature. 2009 Sep 10;461(7261):212-7
19741702
Science. 2008 Jun 6;320(5881):1332-6
18535242
Genes Dev. 2003 Aug 1;17(15):1870-81
12897054
J Cell Biol. 2009 Apr 6;185(1):87-100
19349581
Chromosome Res. 2006;14(1):17-25
16506093
Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19732-7
19064912
Annu Rev Biochem. 2009;78:993-1016
19489737
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6506-11
16617109
Nature. 2005 Jul 7;436(7047):138-41
16001076
Genes Dev. 2004 May 15;18(10):1119-30
15155579
EMBO Rep. 2003 Sep;4(9):861-6
12947417
Nature. 1997 Sep 18;389(6648):251-60
9305837
Nat Struct Mol Biol. 2009 Sep;16(9):938-44
19701201
Biochem Cell Biol. 2003 Jun;81(3):91-9
12897842
Nat Genet. 2003 Jul;34(3):287-91
12808455
Mol Cell Biol. 2008 Nov;28(22):6903-18
18794362
Curr Biol. 1997 Dec 1;7(12):930-9
9382846
Epigenetics. 2009 Feb 16;4(2):80-4
19242119
Cell. 2004 Dec 29;119(7):955-67
15620354
Genes Dev. 2009 Jul 1;23(13):1494-504
19571179
Science. 2001 Dec 7;294(5549):2181-6
11739961
Science. 2006 Feb 10;311(5762):844-7
16469925
Science. 1999 Jun 11;284(5421):1790-5
10364545
Nat Rev Genet. 2009 Mar;10(3):161-72
19204718
J Cell Biol. 2001 Oct 15;155(2):181-5
11604416
Mol Cell. 1999 Feb;3(2):207-17
10078203
Genes Dev. 2009 Feb 15;23(4):452-65
19196654
Curr Opin Struct Biol. 2006 Apr;16(2):213-20
16540311
J Cell Biol. 2005 Jan 3;168(1):41-54
15623580
Science. 2008 Nov 28;322(5906):1384-7
19039137
Curr Biol. 2001 Aug 21;11(16):1227-39
11525737
Biophys J. 2009 Feb 18;96(4):1617-28
19217877
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6428-35
16571659