title: Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo.
abstract: High-order chromatin was reconstituted in vitro. This species reflects the criteria associated with transcriptional regulation in vivo. Histone H1 was determinant to formation of condensed structures, with deacetylated histones giving rise to highly compacted chromatin that approximated 30 nm fibers as evidenced by electron microscopy. Using the PEPCK promoter, we validated the integrity of these templates that were refractory to transcription by attaining transcription through the progressive action of the pertinent factors. The retinoic acid receptor binds to highly compacted chromatin, but the NF1 transcription factor binds only after histone acetylation by p300 and SWI/SNF-mediated nucleosome mobilization, reflecting the in vivo case. Mapping studies revealed the same pattern of nucleosomal repositioning on the PEPCK promoter in vitro and in vivo, correlating with NF1 binding and transcription. The reconstitution of such highly compacted "30 nm" chromatin that mimics in vivo characteristics should advance studies of its conversion to a transcriptionally active form.
authors.affiliation: Department of Biochemistry, New York University School of Medicine, 522 First Avenue, New York, NY 10016, USA.
authors.forename: Guohong
authors.initials: G
authors.lastname: Li
authors.forename: Raphael
authors.initials: R
authors.lastname: Margueron
authors.forename: Guobin
authors.initials: G
authors.lastname: Hu
authors.forename: David
authors.initials: D
authors.lastname: Stokes
authors.forename: Yuh-Hwa
authors.initials: YH
authors.lastname: Wang
authors.forename: Danny
authors.initials: D
authors.lastname: Reinberg
mesh_terms: D000107:Acetylation; D002843:Chromatin / Q000378:metabolism / Q000648:ultrastructure; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D006367:HeLa Cells; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D051839:NFI Transcription Factors / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism; D010729:Phosphoenolpyruvate Carboxykinase (GTP) / Q000235:genetics; D011401:Promoter Regions, Genetic; D018168:Receptors, Retinoic Acid / Q000235:genetics / Q000378:metabolism; D047488:Retinoid X Receptors / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation; D050880:p300-CBP Transcription Factors / Q000235:genetics / Q000378:metabolism; D000099224:p300-CBP-Associated Factor
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; D051839:NFI Transcription Factors; D009707:Nucleosomes; D010729:Phosphoenolpyruvate Carboxykinase (GTP); D018168:Receptors, Retinoic Acid; D047488:Retinoid X Receptors; D014157:Transcription Factors; D050880:p300-CBP Transcription Factors; D000099224:p300-CBP-Associated Factor; C445179:SWI-SNF-B chromatin-remodeling complex
references.citation: Cell. 1998 Jan 9;92(1):105-16
references.pmid: 9489704
references.citation: Mol Cell. 2004 Apr 23;14(2):163-74
references.pmid: 15099516
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8210-5
references.pmid: 15928086
references.citation: J Biol Chem. 1997 Dec 26;272(52):33435-43
references.pmid: 9407140
references.citation: Biol Chem. 2005 Aug;386(8):745-51
references.pmid: 16201869
references.citation: Mol Cell Biol. 2003 Feb;23(3):887-98
references.pmid: 12529394
references.citation: Mol Cell Biol. 2000 Oct;20(20):7541-9
references.pmid: 11003650
references.citation: Mol Cell Biol. 2003 Nov;23(21):7767-79
references.pmid: 14560021
references.citation: Mol Cell Biol. 2003 Jun;23(11):3763-73
references.pmid: 12748280
references.citation: J Biol Chem. 1999 Aug 6;274(32):22563-8
references.pmid: 10428834
references.citation: Cell. 2002 Feb 22;108(4):475-87
references.pmid: 11909519
references.citation: EMBO J. 1995 Apr 18;14(8):1737-51
references.pmid: 7737125
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7934-9
references.pmid: 12034878
references.citation: EMBO J. 2000 Mar 1;19(5):1023-33
references.pmid: 10698943
references.citation: J Steroid Biochem Mol Biol. 2002 Dec;83(1-5):15-23
references.pmid: 12650697
references.citation: Cell. 1985 Oct;42(3):705-11
references.pmid: 2996773
references.citation: J Biol Chem. 1999 Mar 26;274(13):8813-22
references.pmid: 10085123
references.citation: Cell. 2007 Jun 1;129(5):915-28
references.pmid: 17540172
references.citation: Sci Aging Knowledge Environ. 2003 Apr 09;2003(14):RE4
references.pmid: 12844523
references.citation: Mol Cell Endocrinol. 2008 Jan 2;280(1-2):1-5
references.pmid: 17935877
references.citation: Mol Cell. 2004 Nov 5;16(3):439-52
references.pmid: 15525516
references.citation: EMBO J. 1987 Aug;6(8):2321-8
references.pmid: 2822386
references.citation: Mol Biol Cell. 2008 Aug;19(8):3308-22
references.pmid: 18508913
references.citation: Mol Cell. 2003 Dec;12(6):1599-606
references.pmid: 14690611
references.citation: Cell. 1990 Mar 9;60(5):719-31
references.pmid: 2155706
references.citation: Genes Dev. 2009 Jul 1;23(13):1522-33
references.pmid: 19515975
references.citation: Mol Cell. 2002 Feb;9(2):279-89
references.pmid: 11864602
references.citation: J Biol Chem. 2002 Dec 13;277(50):48366-71
references.pmid: 12376534
references.citation: Proc Natl Acad Sci U S A. 1976 Jun;73(6):1897-901
references.pmid: 1064861
references.citation: Science. 2004 Jan 16;303(5656):343-8
references.pmid: 14645854
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 19;102(16):5697-702
references.pmid: 15821029
references.citation: Genes Dev. 1995 Aug 1;9(15):1933-47
references.pmid: 7649476
references.citation: Mol Cell Biol. 2004 Sep;24(18):7891-901
references.pmid: 15340052
references.citation: Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11726-30
references.pmid: 8524837
references.citation: Annu Rev Biochem. 1977;46:931-54
references.pmid: 332067
references.citation: EMBO J. 2008 Mar 19;27(6):817-26
references.pmid: 17962805
references.citation: Mol Cell Biol. 2004 Apr;24(7):3036-47
references.pmid: 15024090
references.citation: Oncogene. 2001 May 28;20(24):3047-54
references.pmid: 11420720
references.citation: Cell. 2003 Dec 12;115(6):751-63
references.pmid: 14675539
references.citation: J Biol Chem. 2005 Oct 7;280(40):34063-72
references.pmid: 16105835
references.citation: Mol Cell. 2000 Nov;6(5):1049-58
references.pmid: 11106744
references.citation: Mol Cell. 1999 Jul;4(1):45-54
references.pmid: 10445026
references.citation: EMBO J. 1998 Jan 2;17(1):244-54
references.pmid: 9427758
references.citation: J Cell Biol. 1979 Nov;83(2 Pt 1):403-27
references.pmid: 387806
references.citation: Science. 1992 Mar 20;255(5051):1573-6
references.pmid: 1347958
references.citation: J Mol Biol. 2008 Sep 12;381(4):816-25
references.pmid: 18653199
references.citation: Nature. 1984 Oct 11-17;311(5986):532-7
references.pmid: 6482966
references.citation: Mol Cell. 2001 Dec;8(6):1219-30
references.pmid: 11779498
references.citation: Science. 2000 Feb 18;287(5456):1262-5
references.pmid: 10678832
references.citation: Cell. 2006 May 19;125(4):703-17
references.pmid: 16713563
references.citation: J Biol Chem. 1998 May 29;273(22):13387-90
references.pmid: 9593667
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6506-11
references.pmid: 16617109
references.citation: J Biol Chem. 2002 Apr 26;277(17):14359-62
references.pmid: 11893728
references.citation: Curr Opin Genet Dev. 2006 Apr;16(2):151-6
references.pmid: 16503135
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Science. 2006 Feb 10;311(5762):844-7
references.pmid: 16469925
references.citation: Cell. 2000 Dec 8;103(6):843-52
references.pmid: 11136970
references.citation: Mol Cell. 2008 Nov 21;32(4):503-18
references.pmid: 19026781
references.citation: Genes Dev. 2001 Nov 1;15(21):2837-51
references.pmid: 11691835
references.citation: Science. 1991 Oct 11;254(5029):238-45
references.pmid: 1718039
references.citation: Curr Opin Struct Biol. 2006 Jun;16(3):336-43
references.pmid: 16714106
references.citation: Mol Cell. 2004 Oct 8;16(1):93-105
references.pmid: 15469825
references.citation: Nucleic Acids Res. 1998 Aug 15;26(16):3657-66
references.pmid: 9685480