Proteome analysis of human nuclear insoluble fractions.
The interphase nucleus is a highly ordered and compartmentalized organelle. Little is known regarding what elaborate mechanisms might exist to explain these properties of the nucleus. Also unresolved is whether some architectural components might facilitate the formation of functional intranuclear compartments or higher order chromatin structure. As the first step to address these questions, we performed an in-depth proteome analysis of nuclear insoluble fractions of human HeLa-S3 cells prepared by two different approaches: a high-salt/detergent/nuclease-resistant fraction and a lithium 3,5-diiodosalicylate/nuclease-resistant fraction. Proteins of the fractions were analyzed by liquid chromatography electrospray ionization tandem mass spectrometry, identifying 333 and 330 proteins from each fraction respectively. Among the insoluble nuclear proteins, we identified 37 hitherto unknown or functionally uncharacterized proteins. The RNA recognition motif, WD40 repeats, HEAT repeats and the SAP domain were often found in these identified proteins. The subcellular distribution of selected proteins, including DEK protein and SON protein, demonstrated their novel associations with nuclear insoluble materials, corroborating our MS-based analysis. This study establishes a comprehensive catalog of the nuclear insoluble proteins in human cells. Further functional analysis of the proteins identified in our study will significantly improve our understanding of the dynamic organization of the interphase nucleus.
Takata
Hideaki
H
Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan.
Nishijima
Hitoshi
H
Ogura
Shun-Ichiro
S
Sakaguchi
Takehisa
T
Bubulya
Paula A
PA
Mochizuki
Tohru
T
Shibahara
Kei-Ichi
K
D002467:Cell Nucleus / Q000737:chemistry / Q000378:metabolism*; D002853:Chromatography, Liquid; D005455:Fluorescent Antibody Technique; D006367:HeLa Cells; D006801:Humans; D007399:Interphase; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism; D020543:Proteome; D012995:Solubility; D021241:Spectrometry, Mass, Electrospray Ionization; D013347:Subcellular Fractions / Q000737:chemistry / Q000378:metabolism; D053719:Tandem Mass Spectrometry
D009687:Nuclear Proteins; D020543:Proteome
J Cell Sci. 2001 Feb;114(Pt 3):463-74
11171316
Trends Biochem Sci. 2000 Mar;25(3):112-4
10694879
J Cell Biol. 2006 Feb 13;172(4):541-52
16476775
Mol Biol Cell. 2004 Aug;15(8):3876-90
15169873
J Cell Biol. 1999 Aug 9;146(3):531-42
10444063
Nat Genet. 2002 Mar;30(3):329-34
11850619
Trends Cell Biol. 2006 Jan;16(1):19-26
16325406
J Cell Biol. 1990 Mar;110(3):569-80
2307700
Genome Res. 2000 Oct;10(10):1445-52
11042144
Cell. 2007 Feb 23;128(4):787-800
17320514
Annu Rev Biochem. 2003;72:573-608
14527325
Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10312-6
1946450
Nat Genet. 2002 Nov;32(3):347-52
12410231
Gene. 2004 Dec 8;343(1):1-9
15563827
Curr Biol. 2002 Jan 8;12(1):1-11
11790298
Chromosoma. 2005 Feb;113(7):385-97
15609038
Cell. 1982 Jul;29(3):847-58
7151171
J Biol Chem. 2001 Jul 13;276(28):26317-23
11333257
Biochem Cell Biol. 2006 Aug;84(4):418-26
16936815
Trends Biochem Sci. 1999 May;24(5):181-5
10322433
Science. 2008 Dec 12;322(5908):1713-7
18948503
J Mol Biol. 2001 May 25;309(1):1-18
11491282
Mol Cell Biol. 1992 Apr;12(4):1687-97
1549122
Curr Biol. 2006 Apr 18;16(8):825-31
16631592
Science. 2000 Oct 13;290(5490):337-41
11030652
Mol Biol Cell. 2000 Mar;11(3):799-805
10712500
Cell. 1984 Nov;39(1):223-32
6091913
Science. 2003 Sep 5;301(5638):1380-2
12958361
J Cell Biol. 1985 May;100(5):1706-15
2985625
Anal Chem. 1996 Mar 1;68(5):850-8
8779443
Nat Rev Mol Cell Biol. 2003 Aug;4(8):605-12
12923522
FEBS J. 2005 May;272(9):2118-31
15853797
Nat Rev Genet. 2007 Feb;8(2):104-15
17230197
Cold Spring Harb Symp Quant Biol. 1993;58:755-65
7525148
Biochem Biophys Res Commun. 1974 Oct 23;60(4):1410-7
4214419
EMBO Rep. 2006 Sep;7(9):874-9
16953200
J Cell Physiol. 1999 Mar;178(3):284-95
9989774
Adv Enzyme Regul. 2002;42:39-52
12123705
Cell. 1992 Sep 18;70(6):949-59
1525831
Trends Cell Biol. 2006 Aug;16(8):391-6
16828286