Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors

Molecular Biology of the Cell - Tập 13 Số 6 - Trang 1977-2000 - 2002
Michael L. Whitfield1, Gavin Sherlock2, Alok J. Saldanha2, John I. Murray2, Catherine A. Ball2, Karen E. Alexander3, John C. Matese2, Charles M. Perou4, Myra M. Hurt3, Patrick O. Brown5,6, David Botstein2
1Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA
2Departments of Genetics and
3Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306; and
4Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
5Biochemistry,
6Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305

Tóm tắt

The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic variation during the cell cycle. Hierarchical clustering of the expression patterns revealed coexpressed groups of previously well-characterized genes involved in essential cell cycle processes such as DNA replication, chromosome segregation, and cell adhesion along with genes of uncharacterized function. Most of the genes whose expression had previously been reported to correlate with the proliferative state of tumors were found herein also to be periodically expressed during the HeLa cell cycle. However, some of the genes periodically expressed in the HeLa cell cycle do not have a consistent correlation with tumor proliferation. Cell cycle-regulated transcripts of genes involved in fundamental processes such as DNA replication and chromosome segregation seem to be more highly expressed in proliferative tumors simply because they contain more cycling cells. The data in this report provide a comprehensive catalog of cell cycle regulated genes that can serve as a starting point for functional discovery. The full dataset is available at http://genome-www.stanford.edu/Human-CellCycle/HeLa/ .

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Tài liệu tham khảo

Abrieu A., 2000, Cell, 102, 817, 10.1016/S0092-8674(00)00070-2

Abrieu A., 2001, Cell, 106, 83, 10.1016/S0092-8674(01)00410-X

Adolph K.W., 1982, J. Biol. Chem., 257, 9086, 10.1016/S0021-9258(18)34246-7

Alizadeh A.A., 2000, Nature, 403, 503, 10.1038/35000501

Alter O., 2000, Proc. Natl. Acad. Sci. USA, 97, 10101, 10.1073/pnas.97.18.10101

Anastasiadis P.Z., 2001, Curr. Opin. Cell Biol., 13, 604, 10.1016/S0955-0674(00)00258-1

Archer S.Y., 1999, Curr. Opin. Genet. Dev., 9, 171, 10.1016/S0959-437X(99)80026-4

Ashburner M., 2000, Nat. Genet., 25, 25, 10.1038/75556

Bai C., 1994, EMBO J., 13, 6087, 10.1002/j.1460-2075.1994.tb06955.x

Barbacid M., 1990, Eur. J. Clin. Invest., 20, 225, 10.1111/j.1365-2362.1990.tb01848.x

Bischoff J.R., 1998, EMBO J., 17, 3052, 10.1093/emboj/17.11.3052

Bishop J.M., 1991, Cell, 64, 235, 10.1016/0092-8674(91)90636-D

Bjorklund S., 1990, Biochemistry, 29, 5452, 10.1021/bi00475a007

Carazo-Salas R.E., 1999, Nature, 400, 178, 10.1038/22133

Cho R.J., 1998, Mol. Cell, 2, 65, 10.1016/S1097-2765(00)80114-8

Cho R.J., 2001, Nat. Genet., 27, 48, 10.1038/83751

Cleveland D.W., 1989, Curr. Opin. Cell Biol., 1, 1148, 10.1016/S0955-0674(89)80065-1

Crawford D.F., 2001, J. Biol. Chem., 276, 37166, 10.1074/jbc.M103414200

Dalton S., 1992, EMBO J., 11, 1797, 10.1002/j.1460-2075.1992.tb05231.x

Davenport J.W., 1999, Genomics, 55, 113, 10.1006/geno.1998.5629

Der C.J., 1982, Proc. Natl. Acad. Sci. USA, 79, 3637, 10.1073/pnas.79.11.3637

Dominski Z., 1999, Mol. Cell Biol., 19, 3561, 10.1128/MCB.19.5.3561

Eisen M.B., 1999, Methods Enzymol., 303, 179, 10.1016/S0076-6879(99)03014-1

Eisen M.B., 1998, Proc. Natl. Acad. Sci. USA, 95, 14863, 10.1073/pnas.95.25.14863

Eliassen K.A., 1998, Mol. Cell. Biol., 18, 7106, 10.1128/MCB.18.12.7106

Engers R., 2000, J. Cancer Res. Clin. Oncol., 126, 682, 10.1007/s004320000148

Fisher R.P., 1994, Cell, 78, 713, 10.1016/0092-8674(94)90535-5

Fonagy A., 1993, J. Cell Physiol., 154, 16, 10.1002/jcp.1041540104

Fontijn R.D., 2001, Mol. Cell Biol., 21, 2944, 10.1128/MCB.21.8.2944-2955.2001

Georgakopoulos A., 1999, Mol. Cell, 4, 893, 10.1016/S1097-2765(00)80219-1

Goswami P.C., 1996, Mol. Cell. Biol., 16, 1500, 10.1128/MCB.16.4.1500

Grosheva I., 2001, J. Cell Sci., 114, 695, 10.1242/jcs.114.4.695

Gruss O.J., 2001, Cell, 104, 83, 10.1016/S0092-8674(01)00193-3

Guenette S., 1995, J. Cell Sci., 108, 1195, 10.1242/jcs.108.3.1195

Gyuris J., 1993, Cell, 75, 791, 10.1016/0092-8674(93)90498-F

Harris M.E., 1991, Mol. Cell. Biol., 11, 2416, 10.1128/MCB.11.5.2416

Heintz N., 1983, Mol. Cell. Biol., 3, 539, 10.1128/MCB.3.4.539

Hetzer M., 2000, Mol. Cell, 5, 1013, 10.1016/S1097-2765(00)80266-X

Hinchcliffe E.H., 2001, Genes Dev., 15, 1167, 10.1101/gad.894001

Hirai H., 1995, Mol. Cell. Biol., 15, 2672, 10.1128/MCB.15.5.2672

Hirose K., 2001, J. Biol. Chem., 276, 5821, 10.1074/jbc.M007252200

Hiyama H., 1998, Oncogene, 16, 1513, 10.1038/sj.onc.1201667

Holtrich U., 1994, Proc. Natl. Acad. Sci. USA, 91, 1736, 10.1073/pnas.91.5.1736

Hoque M.T., 2001, J. Biol. Chem., 276, 5059, 10.1074/jbc.M007809200

Horne M.C., 1996, J. Biol. Chem., 271, 6050, 10.1074/jbc.271.11.6050

Hunter T., 1997, Cell, 88, 333, 10.1016/S0092-8674(00)81872-3

Ishida S., 2001, Mol. Cell. Biol., 21, 4684, 10.1128/MCB.21.14.4684-4699.2001

Iyer V.R., 1999, Science, 283, 83, 10.1126/science.283.5398.83

Jackman M., 1995, EMBO J., 14, 1646, 10.1002/j.1460-2075.1995.tb07153.x

Jinno S., 1994, EMBO J., 13, 1549, 10.1002/j.1460-2075.1994.tb06417.x

Jockusch B.M., 1981, Proc. Natl. Acad. Sci. USA, 78, 3005, 10.1073/pnas.78.5.3005

Kaczmarek L., 1986, Lab. Invest., 54, 365

Kimura M., 1997, J. Biol. Chem., 272, 13766, 10.1074/jbc.272.21.13766

Kinch M.S., 1995, J. Cell Biol., 130, 461, 10.1083/jcb.130.2.461

Knehr M., 1995, Exp. Cell Res., 217, 546, 10.1006/excr.1995.1121

Kondili K., 1996, Eur. J. Biochem., 242, 67, 10.1111/j.1432-1033.1996.0067r.x

Lane H.A., 1996, J. Cell Biol., 135, 1701, 10.1083/jcb.135.6.1701

Laub M.T., 2000, Science, 290, 2144, 10.1126/science.290.5499.2144

Lee M.G., 1987, Nature, 327, 31, 10.1038/327031a0

Lee K.S., 1995, Mol. Cell. Biol., 15, 7143, 10.1128/MCB.15.12.7143

Lei M., 2001, J. Cell Sci., 114, 1447, 10.1242/jcs.114.8.1447

Lengauer C., 1998, Nature, 396, 643, 10.1038/25292

Leone G., 1998, Genes Dev., 12, 2120, 10.1101/gad.12.14.2120

Lew D.J., 1991, Cell, 66, 1197, 10.1016/0092-8674(91)90042-W

Li F., 1999, Cancer Res., 59, 3143

Li J., 1997, Cell, 90, 917, 10.1016/S0092-8674(00)80356-6

Liao H., 1995, J. Cell Biol., 130, 507, 10.1083/jcb.130.3.507

Lucibello F.C., 1995, EMBO J., 14, 132, 10.1002/j.1460-2075.1995.tb06983.x

Ma T., 2000, Genes Dev., 14, 2298, 10.1101/gad.829500

Marra G., 1996, Oncogene, 13, 2189

Marzluff W.F., 1992, Gene Expression, 2, 93

Marzluff W.F., 1988, Trends Biochem. Sci., 13, 49, 10.1016/0968-0004(88)90027-8

Masuda H., 1996, J. Biochem., 120, 415, 10.1093/oxfordjournals.jbchem.a021428

Matsuoka M., 1994, Mol. Cell. Biol., 14, 7265, 10.1128/MCB.14.11.7265

Mitchell J.R., 1999, Nature, 402, 551, 10.1038/990141

Morris G.F., 1989, J. Biol. Chem., 264, 13856, 10.1016/S0021-9258(18)80079-5

Muchardt C., 2001, Oncogene, 20, 3067, 10.1038/sj.onc.1204331

Nachury M.V., 2001, Cell, 104, 95, 10.1016/S0092-8674(01)00194-5

Nurse P., 2000, Cell, 100, 71, 10.1016/S0092-8674(00)81684-0

Ohtani K., 1995, Proc. Natl. Acad. Sci. USA, 92, 12146, 10.1073/pnas.92.26.12146

Okuda T., 1995, Genomics, 29, 623, 10.1006/geno.1995.9957

Ouyang B., 1998, Cell Growth Differ., 9, 877

Pei L., 1997, Mol. Endocrinol., 11, 433, 10.1210/mend.11.4.9911

Perou C.M., 1999, Proc. Natl. Acad. Sci. USA, 96, 9212, 10.1073/pnas.96.16.9212

Perou C.M., 2000, Nature, 406, 747, 10.1038/35021093

Pines J., 1989, Cell, 58, 833, 10.1016/0092-8674(89)90936-7

Pines J., 1990, Nature, 346, 760, 10.1038/346760a0

Plumb M., 1983, Nucleic Acids Res., 11, 2391, 10.1093/nar/11.8.2391

Pruitt K.D., 2001, Nucleic Acids Res., 29, 137, 10.1093/nar/29.1.137

Puck T.T., 1956, J. Exp. Med., 103, 273, 10.1084/jem.103.2.273

Rajan J.V., 1996, Proc. Natl. Acad. Sci. USA, 93, 13078, 10.1073/pnas.93.23.13078

Richardson R.T., 2000, J. Biol. Chem., 275, 30378, 10.1074/jbc.M003781200

Richardson H.E., 1990, Genes Dev., 4, 1332, 10.1101/gad.4.8.1332

Rodriguez Fernandez J.L., 1992, J. Cell Biol., 119, 427, 10.1083/jcb.119.2.427

Ross D.T., 2000, Nat. Genet., 24, 227, 10.1038/73432

Rudiger M., 1998, Bioessays, 20, 733, 10.1002/(SICI)1521-1878(199809)20:9<733::AID-BIES6>3.0.CO;2-H

Saha P., 1998, J. Biol. Chem., 273, 18205, 10.1074/jbc.273.29.18205

Sardet C., 1995, Proc. Natl. Acad. Sci. USA, 92, 2403, 10.1073/pnas.92.6.2403

Scheffner M., 1991, Proc. Natl. Acad. Sci. USA, 88, 5523, 10.1073/pnas.88.13.5523

Schneiderman M.H., 1972, Exp. Cell Res., 74, 430, 10.1016/0014-4827(72)90398-9

Schumperli D., 1988, Trends Genet., 4, 187, 10.1016/0168-9525(88)90074-1

Shah J.V., 2000, Cell, 103, 997, 10.1016/S0092-8674(00)00202-6

Shelby R.D., 1997, J. Cell Biol., 136, 501, 10.1083/jcb.136.3.501

Sherlock G., 2001, Nucleic Acids Res., 29, 152, 10.1093/nar/29.1.152

Shindo M., 1998, Biochem. Biophys. Res. Commun., 244, 285, 10.1006/bbrc.1998.8250

Slansky J.E., 1996, Bioessays, 18, 55, 10.1002/bies.950180111

Smith M.R., 1997, Biochem. Biophys. Res. Commun., 234, 397, 10.1006/bbrc.1997.6633

10.1091/mbc.9.12.3273

Stampfer M.R., 1993, Exp. Cell Res., 208, 175, 10.1006/excr.1993.1236

Stillman B., 1996, Science, 274, 1659, 10.1126/science.274.5293.1659

Takai N., 2001, Cancer Lett., 164, 41, 10.1016/S0304-3835(00)00703-5

Tassan J.P., 1994, J. Cell Biol., 127, 467, 10.1083/jcb.127.2.467

Tobey R.A., 1988, Exp. Cell Res., 179, 400, 10.1016/0014-4827(88)90279-0

Troyanskaya O., 2001, Bioinformatics, 17, 520, 10.1093/bioinformatics/17.6.520

Vareli K., 2000, Exp. Cell Res., 257, 152, 10.1006/excr.2000.4857

Vaughn J.P., 1996, Cancer Res., 56, 4590

Wang E., 2000, Nat. Biotechnol., 18, 457, 10.1038/74546

Wang Z.-F., 1996, Genes Dev., 10, 3028, 10.1101/gad.10.23.3028

Wang W., 1996, Genes Dev., 10, 2117, 10.1101/gad.10.17.2117

Weinstein J., 1997, J. Biol. Chem., 272, 28501, 10.1074/jbc.272.45.28501

Weinstein J., 1994, Mol. Cell. Biol., 14, 3350, 10.1128/MCB.14.5.3350

Wells D., 1985, Proc. Natl. Acad. Sci. USA, 82, 2834, 10.1073/pnas.82.9.2834

Whitfield M.L., 2000, Mol. Cell. Biol., 20, 4188, 10.1128/MCB.20.12.4188-4198.2000

Wiese C., 2001, Science, 291, 653, 10.1126/science.1057661

Wilkins J.A., 1982, Cell, 28, 83, 10.1016/0092-8674(82)90377-4

Williams G.H., 1998, Proc. Natl. Acad. Sci. USA, 95, 14932, 10.1073/pnas.95.25.14932

Wittmann T., 2001, Nat. Cell Biol., 3, E28, 10.1038/35050669

Wood K.W., 1997, Cell, 91, 357, 10.1016/S0092-8674(00)80419-5

Yamamoto T., 1997, J. Cell Biol., 139, 785, 10.1083/jcb.139.3.785

Yamamoto T., 1999, J. Biochem., 126, 799, 10.1093/oxfordjournals.jbchem.a022519

Yan Z., 1998, Proc. Natl. Acad. Sci. USA, 95, 3603, 10.1073/pnas.95.7.3603

Zariwala M., 1998, Oncogene, 17, 2787, 10.1038/sj.onc.1202505

Zhao J., 1998, Genes Dev., 12, 456, 10.1101/gad.12.4.456

Zhao J., 2000, Genes Dev., 14, 2283, 10.1101/gad.827700

10.1091/mbc.8.11.2329

Zhou H., 1998, Nat. Genet., 20, 189, 10.1038/2496

Zieve G.W., 1980, Exp. Cell Res., 126, 397, 10.1016/0014-4827(80)90279-7

Zou H., 1999, Science, 285, 418, 10.1126/science.285.5426.418

Zwicker J., 1995, EMBO J., 14, 4514, 10.1002/j.1460-2075.1995.tb00130.x

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Molecular Biology of the Cell

Tập 13 Số 6

1977-2000

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