Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes

Nucleic Acids Research

Volumn 36, Issue 1, 2008, Pages 189-202

  Harada, Ryoko ^a   Vadnais, Charles ^a,b   Sansregret, Laurent ^a,b   Leduy, Lam ^a   Bérubé, Ginette ^a   Robert, François ^b   Nepveu, Alain ^a,b  

^a MCGILL UNIVERSITY HEALTH CENTRE   (Canada)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN P110; RETROVIRUS VECTOR; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CUX1; UNCLASSIFIED DRUG;

ARTICLE; CELL CYCLE PROGRESSION; CELL CYCLE S PHASE; CELL POPULATION; CELL STRAIN 3T3; CELL STRAIN HEK293; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA REPLICATION; EPSTEIN BARR VIRUS; GENE ACTIVATION; GENE EXPRESSION; GENE LOCATION; GENE REPRESSION; GENE TARGETING; GENETIC ANALYSIS; HELA CELL; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DEGRADATION; PROTEIN TRANSPORT;

ANIMALS; CELL LINE; CHROMATIN; CHROMATOGRAPHY, AFFINITY; DNA REPLICATION; GENES, CDC; GENOMICS; HOMEODOMAIN PROTEINS; HUMANS; MICE; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); REPRESSOR PROTEINS; S PHASE; SEQUENCE ANALYSIS, DNA; TRANS-ACTIVATION (GENETICS);

HUMAN HERPESVIRUS 4;

EID: 38349195017     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm970     Document Type: Article

References (51)

1. Nepveu,A. (2001) Role of the multifunctional CDP/Cut/Cux homeodomain transcription factor in regulating differentiation, cell growth and development. Gene, 270, 1-15.
2. Goulet,B., Baruch,A., Moon,N.S., Poirier,M., Sansregret,L.L., Erickson,A., Bogyo,M. and Nepveu,A. (2004) A Cathepsin L isoform that is devoid of a signal peptide localizes to the nucleus in S phase and processes the CDP/Cux transcription factor. Mol. Cell, 14, 207-219.
3. Maitra,U., Seo,J., Lozano,M.M. and Dudley,J.P. (2006) Differentiation-induced cleavage of Cut11l/CDP generates a novel dominant-negative isoform that regulates mammary gene expression. Mol. Cell. Biol., 26, 7466-7478.
4. Moon,N.S., Premdas,P., Truscott,M., Leduy,L., Berube,G. and Nepveu,A. (2001) S Phase-Specific Proteolytic Cleavage Is Required to Activate Stable DNA Binding by the CDP/Cut Homeodomain Protein. Mol. Cell. Biol., 21, 6332-6345.
5. Neufeld,E.J., Skalnik,D.G., Lievens,P.M. and Orkin,S.H. (1992) Human CCAAT displacement protein is homologous to the Drosophila homeoprotein, cut. Nat. Genet., 1, 50-55.
6. Moon,N.S., Berube,G. and Nepveu,A. (2000) CCAAT displacement activity involves Cut repeats 1 and 2, not the Cut homeodomain. J. Biol. Chem. 275, 31325-31334.
7. Skalnik,D.G., Strauss,E.C. and Orkin,S.H. (1991) CCAAT displacement protein as a repressor of the myelomonocytic-specific gp91-phox gene promoter. J. Biol. Chem., 266, 16736-16744.
8. Lievens,P.M.J., Donady,J.J., Tufarelli,C. and Neufeld,E.J. (1995) Repressor activity of CCAAT displacement protein in HL-60 myeloid leukemia cells. J. Biol. Chem., 270, 12745-12750.
9. Superti-Furga,G., Barberis,A., Schreiber,E. and Busslinger,M. (1989) The protein CDP, but not CP1, Footprints on the CCAAT region of the g-globulin gene in unfractionated. B-cell extracts. Biochim. Biophys. Acta, 1007, 237-242.
10. Stunkel,W., Huang,Z., Tan,S.H., O'Connor,M.J. and Bernard,H.U. (2000) Nuclear matrix attachment regions of human papillomavirus type 16 repress or activate the E6 promoter, depending on the physical state of the viral DNA. J. Virol., 74, 2489-2501.
11. Pattison,S., Skalnik,D.G. and Roman,A. (1997) Ccaat displacement protein, a regulator of differentiation-specific gene expression, binds a negative regulatory element within the 5′ end of the human papillomavirus type 6 kong control region. J. Virol., 71, 2013-2022.
12. Truscott,M., Raynal,L., Premdas,P., Goulet,B., Leduy,L., Berube,G. and Nepveu,A. (2003) CDP/Cux stimulates transcription from the DNA polymerase alpha gene promoter. Mol. Cell. Biol., 23, 3013-3028.
13. Truscott,M., Raynal,L., Wang,Y., Berube,G., Leduy,L. and Nepveu,A. (2004) The N-terminal region of the CCAAT displacement protein (CDP)/Cux transcription factor functions as an autoinhibitory domain that modulates DNA binding. J. Biol. Chem., 279, 49787-49794.
14. Ledford,A.W., Brantley,J.G., Kemeny,G., Foreman,T.L., Quaggin,S.E., Igarashi,P., Oberhaus,S.M., Rodova,M., Calvet,J.P. et al. (2002) Deregulated expression of the homeobox gene Cux-1 in transgenic mice results in downregulation of p27(kip1) expression huring nephrogenesis, glomerular abnormalities, and multiorgan hyperplasia. Dev. Biol., 245, 157-171.
15. Cadieux,C., Fournier,S., Peterson,A.C., Bédard,C., Bedell,B.J. and Nepveu,A. (2006) Transgenic mice expressing the p75 CCAAT-displacement protein/cut homeobox isoform develop a myeloproliferative disease-like myeloid leukemia. Cancer Res., 66, 9492-9501.
16. Ellis,T., Gambardella,L., Horcher,M., Tschanz,S., Capol,J., Bertram,P., Jochum,W., Barrandon,Y. and Busslinger,M. (2001) The transcriptional repressor CDP (Cut11) is essential for epithelial cell differentiation of the lung and the hair follicle. Genes Dev., 15, 2307-2319.
17. Luong,M.X., van der Meijden,C.M., Xing,D.,Hesselton,R., Monuki,E.S., Jones,S.N., Lian,J.B., Stein,J.L., Stein,G.S. et al. (2002) Genetic ablation of the CDP/Cux protein C terminus results in hair cycle defects and reduced male fertility. Mol. Cell. Biol., 22, 1424-1437.
18. Sinclair,A.M., Lee,J.A., Goldstein,A., Xing,D., Liu,S., Ju,R., Tucker,P.W., Neufeld,E.J. and Scheuermann,R.H. (2001) Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice. Blood, 98, 3658-3667.
19. Michl,P., Ramjaun,A.R., Pardo,O.E., Warne,P.H., Wagner,M., Poulsom,R., D'Arrigo,C., Ryder.K., Menke,A. et al. (2005) CUTL1 is a target of TGF(beta) signaling that enhances cancer cell motility and invasiveness. Cancer Cell, 7, 521-532.
20. Sansregret,L., Goulet,B., Harada,R., Wilson,B., Leduy,L., Bertoglio,J. and Nepveu,A. (2006) The p110 isoform of the CDP/Cux transcription factor accelerates entry into S phase. Mol. Cell. Biol., 26, 2441-2455.
21. van Wijnen,A.J., Wright,K.L., Lian,J.B., Stein,J.L. and Stein,G.S. (1989) Human H4 histone gene transcription requires the proliferation-specific nuclear factor HiNF-D. Auxiliary roles for HiNF-C (Sp1-like) and HiNF-A (high mobility group-like). J. Biol. Chem., 264, 15034-15042.
22. Holthuis,J., Owen,T.A., van Wijnen,A.J., Wright,K.L., Ramsey-Ewing,A., Kennedy,M.B., Carter,R., Cosenza,S.C., Soprano,K.J. et al. (1990) Tumor cells exhibit deregulation of the cell cycle histone gene promoter factor HiNF-D. Science, 247, 1454-1457.
23. van Wijnen,A.J., Owen,T.A., Holthuis,J., Lian,J.B., Stein,J.L. and Stein,G.S. (1991) Coordination of protein-DNA interactions in the promoters of hurian H4, H3, and H1 histone genes during the cell cycle, tumorigenesis, and, development. J. Cell. Physiol., 148, 174-189.
24. Wright,K.L., Dell'Orco,R.T., van Wijnen,A.J., Stein,J.L. and Stein,G.S. (1992) Multiple mechanisms regulate the proliferation-specific histone gene transcription factor HiNF-D in normal human diploid fibroblasts. Biochemistry, 31, 2812-2818.
25. van Wijnen,A.J., van Gurp,M.F., de Ridder,M.C., Tufarelli,C., Last,T.J., Bimbaum,M., Vaughan,P.S., Giordano,A., Krek,W. et al. (1996) CDP/ cut is the DNA-binding subunit of histone gene transcription factor HiNF-D: A mechanism for gene regulation at the G1/S phase cell cycle transition point independent of transcription factor E2F. Proc. Natl Acad. Sci. USA, 93, 11516-11521.
26. Coqueret,O., Berube,G. and Nepveu,A. (1998) The mammalian Cut homeodomain protein functions as a cell-cycle dependent transcriptional repressor which downmodulates p21WAF1/CIP1/SDI1 in S phase. EMBO J. 17, 4680-4694.
27. Santaguida,M., Ding,Q., Berube,G., Truscott,M., Whyte,P. and Nepveu,A. (2001) Phosphorylation of the CCAAT displacement protein (CDP)/Cux transcription factor by cyclin A-Cdk1 modulates its DNA binding activity in G(2). J. Biol. Chem., 276, 45780-45790.
28. Santaguida,M. and Nepveu,A. (2005) Differential regulation of CDP/Cux p110 by cychn A/Cdk2 and cyclin A/Cdk1. J. Biol. Chem., 280, 32712-32721.
29. Weinmann,A.S. and Farnham,P.J. (2002) Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods, 26, 37-47.
30. Puig,O., Caspary,F., Rigaut,G., Rutz,B., Bouveret,E., Bragado-Nilsson,E., Wilm,M. and Seraphin,B. (2001) The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods, 24, 218-229.
31. Ren,B., Cam,H., Takahashi,Y., Volkert,T., Terragni,J., Young,R.A. and Dynlacht,B.D. (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev., 16, 245-256.
32. Laganiere,J., Deblois,G., Lefebvre,C., Bataille,A.R., Robert,F. and Giguere,V. (2005) From the cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc. Natl Acad. Sci. USA, 102, 11651-11656.
33. Odom,D.T., Zizlsperger,N., Gordon,D.B., Bell,G.W., Rinaldi,N.J., Murray,H.L., Volkert,T.L., Schreiber,J., Rolfe,P.A. et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science, 303, 1378-1381.
34. Philippe,J. (1994) The southwestern assay. Meth. Mol. Biol., 31 349-361.
35. Shire,K., Ceccarelli,D.F., Avolio-Hunter,T.M. and Frappier,L. (1999) EBP2, a human protein that interacts with sequences of the Epstein-Barr virus nuclear antigen 1 important for plasmid maintenance. J. Virol. 73, 2587-2595.
36. Rigaut,G., Shevchenko,A., Rutz,B., Wilm,M., Mann,M. and Seraphin,B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 17 1030-1032.
37. Geck,P., Maffini,M.V., Szelei,J., Sonnenschein,C. and Soto,A.M. (2000) Androgen-induced proliferative quiescence in prostate cancer cells: The role of AS3 as its mediator. Proc. Natl Acad. Sci. USA, 97, 10185-10190.
38. Saqr,H.E., Omran,O., Dasgupta,S., Yu,R.K., Oblinger,J.L. and Yates,A.J. (2006) Endogenous GD3 ganglioside induces apoptosis in U-1242 MG glioma. cells. J. Neurochem., 96, 1301-1314.
39. Sipione,S., Rigamonti,D., Valenza,M., Zuccato,C., Conti,L., Pritchard,J., Kooperberg,C., Olson,J.M. and Cattaneo,E. (2002) Early transcriptional profiles in huntingtin-inducible striatal cells by microarray analyses. Hum. Mol. Genet., 11, 1953-1965.
40. Goulet,B., Sansregret,L., Leduy,L., Bogyo,M., Weber,E., Chauhan,S.S. and Nepveu,A. (2007) Increased expression and activity of nuclear cathepsin L in cancer cells suggests a novel mechanism of cell transformation. Mol. Cancer Res., 5, 899-907.
41. Harada,R., Berube,G., Tamplin,O.J., Denis-Larose,C. and Nepveu,A. (1995) DNA-binding specificity of the cut repeats from the human cut-like protein. Mol. Cell. Biol., 15, 129-140.
42. Matys,V., Kel-Margoulis,O.V., Fricke,E., Liebich,I., Land,S., Barre-Dirrie,A., Reuter,I., Chekmenev,D., Krull,M. et al. (2006) TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, 13108-13110.
43. Andres,Y., Chiara,M.D. and Mahdavi,V. (1994) A new bipartite DNA-binding domain: Cooperative interaction between the cut repeat and homeo domain of the cut homeo proteins. Genes Dev., 8, 245-257.
44. Aufiero,B., Neufeld,E.J. and Orkin,S.H. (1994) Sequence-specific DNA binding of individual Cut repeats of the human CCAAT displacement/Cut homeodomain protein. Proc. Natl Acad Sci. USA, 91, 7757-7761.
45. Li,S., Moy,L., Pittman,N., Shue,G., Aufiero,B., Neufeld,E.J., LeLeiko,N.S. and Walsh,M.J. (1999) Transcriptional repression of the cystic fibrosis transmembrane conductance regulator gene, mediated by CCAAT displacement protein/cut homolog, is associated with histone deacetylation. J. Biol. Chem., 274, 7803-7815.
46. Nishio,H. and Walsh,M.J. (2004) CCAAT displacement protein/cut homolog recruits G9a histone lysine methyltransferase to repress transcription. Proc. Natl Acad. Sci. USA, 101, 11257-11262.
47. Yates,J.L. and Guan,N. (1991) Epstein-Barr virus-derived plasmids replicate only once per cell cycle and are not amplified after entry into cells. J. Virol., 65, 483-488.
48. Bieda,M., Xu,X., Singer,M.A., Green,R. and Farnham,P.J. (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res., 16, 595-605.
49. Black,E.P., Hallstrom,T., Dressman,H.K., West,M. and Nevins,J.R. (2005) Distinctions in the specificity of E2F function revealed by gene expression signatures. Proc. Natl Acad. Sci. USA, 102, 15948-15953.
50. Zhu,W., Giangrande, P.H. and Nevins,J.R. (2004) E2Fs link the control of G1/S and G2/M transcription. EMBO J., 23, 4615-4626.
51. Zwicker,J., Lucibello,F.C., Wolfraim,L.A., Gross,C., Truss,M., Engeland,K. and Muller,R. (1995) Cell cycle regulation of the cyclin A, cdc25C and cdc2 genes is based on a common mechanism of transcriptional repression. EMBO J., 14, 4514-4522.