Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis

Nucleic Acids Research

Volumn 39, Issue 22, 2011, Pages 9536-9548

  Gorski, Julia J ^a   Savage, Kienan I ^a   Mulligan, Jude M ^b   McDade, Simon S ^a   Blayney, Jaine K ^a   Ge, Zhaoping ^b   Harkin, D Paul ^a,b  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b Almac Sciences   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; DNA; PROTEIN ZF5; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTION FACTOR AP 2 ALPHA; TRANSCRIPTION FACTOR PAX2; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL STRAIN MCF 7; CHIP CHIP ANALYSIS; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC TRANSFECTION; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DEPLETION; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN INTERACTION; TRANSCRIPTION REGULATION;

BRCA1 PROTEIN; CELL LINE, TUMOR; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 83755205418     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr679     Document Type: Article

References (51)

1. Monteiro,A.N., August,A. and Hanafusa,H. (1996) Evidence for a transcriptional activation function of BRCA1 C-terminal region. Proc. Natl Acad. Sci. USA, 93, 13595-13599. (Pubitemid 26424164)
2. Humphrey,J.S., Salim,A., Erdos,M.R., Collins,F.S., Brody,L.C. and Klausner,R.D. (1997) Human BRCA1 inhibits growth in yeast: potential use in diagnostic testing. Proc. Natl Acad. Sci. USA, 94, 5820-5825. (Pubitemid 27241855)
3. Anderson,S.F., Sclegel,B.P., Nakajima,T., Wolpin,E.S. and Parvin,J.D. (1998) BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A. Nat. Genet., 19, 254-256. (Pubitemid 28309336)
4. Scully,R., Anderson,S.F., Chao,D.M., Wei,W., Ye,L., Young,R.A., Livingston,D.M. and Parvin,J.D. (1997) BRCA1 is a component of the RNA polymerase II holoenzyme. Proc. Natl Acad. Sci. USA., 94, 5605-5610. (Pubitemid 27241816)
5. Wang,Y., Cortez,D., Yazdi,P., Neff,N., Elledge,S.J. and Qin,J. (2000) BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev., 14, 927-939. (Pubitemid 30253002)
6. Fabbro,M., Savage,K., Hobson,K., Deans,A.J., Powell,S.N., McArthur,G.A. and Khanna,K.K. (2004) BRCA1-BARD1 complexes are required for p53Ser-15 phosphorylation and a G1/S arrest following ionizing radiation-induced DNA damage. J. Biol. Chem., 279, 31251-31258. (Pubitemid 39037790)
7. Fan,S., Ma,Y.X., Wang,C., Yuan,R.-q., Meng,Q., Wang,J.-A., Erdos,M., Goldberg,I.D., Webb,P., Kushner,P.J. et al. (2001) Role of direct interaction in BRCA1 inhibition of estrogen receptor activity. Oncogene, 20, 77-87. (Pubitemid 32142340)
8. Zheng,L., Annab,L.A., Afshari,C.A., Lee,W.H. and Boyer,T.G. (2001) BRCA1 mediates ligand-independent transcriptional repression of the estrogen receptor. Proc. Natl Acad. Sci. USA, 98, 9587-9592. (Pubitemid 32769347)
9. Kennedy,R.D., Gorski,J.J., Quinn,J.E., Stewart,G.E., James,C.R., Moore,S., Mulligan,K., Emberley,E.D., Lioe,T.F., Morrison,P.J. et al. (2005) BRCA1 and c-Myc associate to transcriptionally repress psoriasin, a DNA damage-inducible gene. Cancer Res., 65, 10265-10272. (Pubitemid 41743718)
10. Hosey,A.M., Gorski,J.J., Murray,M.M., Quinn,J.E., Chung,W.Y., Stewart,G.E., James,C.R., Farragher,S.M., Mulligan,J.M., Scott,A.N. et al. (2007) Molecular basis for estrogen receptor alpha deficiency in BRCA1-linked breast cancer. J. Natl Cancer Inst., 99, 1683-1694. (Pubitemid 351767217)
11. Gorski,J.J., James,C.R., Quinn,J.E., Stewart,G.E., Staunton,K.C., Buckley,N.E., McDyer,F.A., Kennedy,R.D., Wilson,R.H., Mullan,P.B. et al. (2010) BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer. Breast Cancer Res. Treat., 122, 721-731.
12. Lamber,E.P., Horwitz,A.A. and Parvin,J.D. BRCA1 represses amphiregulin gene expression. Cancer Res., 70, 996-1005.
13. Harte,M.T., O'Brien,G.J., Ryan,N.M., Gorski,J.J., Savage,K.I., Crawford,N.T., Mullan,P.B. and Harkin,D.P. (2010) BRD7, a subunit of SWI/SNF complexes, binds directly to BRCA1 and regulates BRCA1-dependent transcription. Cancer Res., 70, 2538-2547.
14. Mullan,P.B., Quinn,J.E. and Harkin,D.P. (2006) The role of BRCA1 in transcriptional regulation and cell cycle control. Oncogene, 25, 5854-5863. (Pubitemid 44453441)
15. Savage,K.I. and Harkin,D.P. (2009) BRCA1 and BRCA2: Role in the DNA Damage Response, Cancer Formation and Treatment. In Shiloh,Y. and Khanna,K.K. (eds), The DNA Damage Response: Implications on Cancer Formation and Treatment, Vol. 1. Springer, Dordrecht, Heidelberg, London, New York, pp. 415-443.
16. Chen,G.-C., Guan,L.-S., Yu,J.-H., Li,G.-C., Kim,H.-R.C. and Wang,Z.-Y. (2001) Rb-associated protein 46 (RbAp46) inhibits transcriptional transactivation mediated by BRCA1. Biochem. Biophys. Res. Comm., 284, 507-514. (Pubitemid 32923060)
17. Yarden,R.I. and Brody,L.C. (1999) BRCA1 interacts with components of the histone deacetylase complex. Proc. Natl Acad. Sci. USA, 96, 4983-4988. (Pubitemid 29214522)
18. Oishi,H., Kitagawa,H., Wada,O., Takezawa,S., Tora,L., Kouzu- Fujita,M., Takada,I., Yano,T., Yanagisawa,J. and Kato,S. (2006) An hGCN5/TRRAP histone acetyltransferase complex co-activates BRCA1 transactivation function through histone modification. J. Biol. Chem., 281, 20-26. (Pubitemid 43671158)
19. Harte,M.T., O'Brien,G.J., Ryan,N.M., Gorski,J.J., Savage,K.I., Crawford,N.T., Mullan,P.B. and Harkin,D.P. BRD7, a subunit of SWI/SNF complexes, binds directly to BRCA1 and regulates BRCA1-dependent transcription. Cancer Res., 70, 2538-2547.
20. Farmer,H., McCabe,N., Lord,C.J., Tutt,A.N., Johnson,D.A., Richardson,T.B., Santarosa,M., Dillon,K.J., Hickson,I., Knights,C. et al. (2005) Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature, 434, 917-921. (Pubitemid 40559006)
21. Bryant,H.E., Schultz,N., Thomas,H.D., Parker,K.M., Flower,D., Lopez,E., Kyle,S., Meuth,M., Curtin,N.J. and Helleday,T. (2005) Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature, 434, 913-917. (Pubitemid 40559005)
22. Weng,L., Dai,H., Zhan,Y., He,Y., Stepaniants,S.B. and Bassett,D.E. (2006) Rosetta error model for gene expression analysis. Bioinformatics, 22, 1111-1121.
23. Hosey,A.M., Gorski,J.J., Murray,M.M., Quinn,J.E., Chung,W.Y., Stewart,G.E., James,C.R., Farragher,S.M., Mulligan,J.M., Scott,A.N. et al. (2007) Molecular basis for estrogen receptor {alpha} deficiency in BRCA1-linked breast cancer. J. Natl Cancer Inst., 99, 1683-1694. (Pubitemid 351767217)
24. Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
25. Ameur,A., Rada-Iglesias,A., Komorowski,J. and Wadelius,C. (2009) Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. Nucleic Acids Res., 37, e85.
26. Ernst,P. and Smale,S.T. (1995) Combinatorial regulation of transcription. I: General aspects of transcriptional control. Immunity, 2, 311-319.
27. De Siervi,A., De Luca,P., Byun,J.S., Di,L.J., Fufa,T., Haggerty,C.M., Vazquez,E., Moiola,C., Longo,D.L. and Gardner,K. (2010) Transcriptional autoregulation by BRCA1. Cancer Res., 70, 532-542.
28. Tan,Y., Raychaudhuri,P. and Costa,R.H. (2007) Chk2 mediates stabilization of the FoxM1 transcription factor to stimulate expression of DNA repair genes. Mol. Cell Biol., 27, 1007-1016. (Pubitemid 46174563)
29. Kennedy,R.D., Gorski,J.J., Quinn,J.E., Stewart,G.E., James,C.R., Moore,S., Mulligan,K., Emberley,E.D., Lioe,T.F., Morrison,P.J. et al. (2005) BRCA1 and c-Myc associate to transcriptionally repress psoriasin, a DNA damage-inducible gene. Cancer Res., 65, 10265-10272. (Pubitemid 41743718)
30. Li,H., Lee,T.-H. and Avraham,H. (2002) A novel tricomplex of BRCA1, Nmi, and c-Myc inhibits c-Myc-induced human telomerase reverse transcriptase gene (hTERT) promoter activity in breast cancer. J. Biol. Chem., 277, 20965-20973. (Pubitemid 34967407)
31. Kumaraswamy,S., Chinnaiyan,P., Shankavaram,U.T., Lu,X., Camphausen,K. and Tofilon,P.J. (2008) Radiation-induced gene translation profiles reveal tumor type and cancer-specific components. Cancer Res., 68, 3819-3826.
32. Hernandez-Vargas,H., von Kobbe,C., Sanchez-Estevez,C., Julian-Tendero,M., Palacios,J. and Moreno-Bueno,G. (2007) Inhibition of paclitaxel-induced proteasome activation influences paclitaxel cytotoxicity in breast cancer cells in a sequence-dependent manner. Cell Cycle, 6, 2662-2668. (Pubitemid 350224050)
33. Vidarsson,H., Mikaelsdottir,E.K., Rafnar,T., Bertwistle,D., Ashworth,A., Eyfjord,J.E. and Valgeirsdottir,S. (2002) BRCA1 and BRCA2 bind Stat5a and suppress its transcriptional activity. FEBS Lett., 532, 247-252. (Pubitemid 35375898)
34. Neish,A.S., Anderson,S.F., Schlegel,B.P., Wei,W. and Parvin,J.D. (1998) Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res., 26, 847-853. (Pubitemid 28291286)
35. Kwok,J.M., Peck,B., Monteiro,L.J., Schwenen,H.D., Millour,J., Coombes,R.C., Myatt,S.S. and Lam,E.W. FOXM1 confers acquired cisplatin resistance in breast cancer cells. Mol. Cancer Res., 8, 24-34.
36. Carr,J.R., Park,H.J., Wang,Z., Kiefer,M.M. and Raychaudhuri,P. FoxM1 mediates resistance to herceptin and paclitaxel. Cancer Res., 70, 5054-5063.
37. Fernandez-Ramires,R., Sole,X., De Cecco,L., Llort,G., Cazorla,A., Bonifaci,N., Garcia,M.J., Caldes,T., Blanco,I., Gariboldi,M. et al. (2009) Gene expression profiling integrated into network modelling reveals heterogeneity in the mechanisms of BRCA1 tumorigenesis. Br. J. Cancer, 101, 1469-1480.
38. Gorski,J.J., James,C.R., Quinn,J.E., Stewart,G.E., Staunton,K.C., Buckley,N.E., McDyer,F.A., Kennedy,R.D., Wilson,R.H., Mullan,P.B. et al. (2010) BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer. Breast Cancer Res. Treat., 122, 721-731.
39. Lamber,E.P., Horwitz,A.A. and Parvin,J.D. (2010) BRCA1 represses amphiregulin gene expression. Cancer Res., 70, 996-1005.
40. Chabalier-Taste,C., Racca,C., Dozier,C. and Larminat,F. (2008) BRCA1 is regulated by Chk2 in response to spindle damage. Biochim. Biophys. Acta., 1783, 2223-2233.
41. Gatei,M., Zhou,B.B., Hobson,K., Scott,S., Young,D. and Khanna,K.K. (2001) Ataxia telangiectasia mutated (ATM) kinase and ATM and Rad3 related kinase mediate phosphorylation of Brca1 at distinct and overlapping sites. In vivo assessment using phospho-specific antibodies. J. Biol. Chem., 276, 17276-17280.
42. Fan,W., Jin,S., Tong,T., Zhao,H., Fan,F., Antinore,M.J., Rajasekaran,B., Wu,M. and Zhan,Q. (2002) BRCA1 regulates GADD45 through its interactions with the OCT-1 and CAAT motifs. J. Biol. Chem., 277, 8061-8067. (Pubitemid 34968259)
43. Zhao,H., Jin,S., Fan,F., Fan,W., Tong,T. and Zhan,Q. (2000) Activation of the transcription factor Oct-1 in response to DNA damage. Cancer Res., 60, 6276-6280.
44. Weake,V.M. and Workman,J.L. Inducible gene expression: diverse regulatory mechanisms. Nat. Rev. Genet., 11, 426-437.
45. Cable,P.L., Wilson,C.A., Calzone,F.J., Rauscher,F.J. III, Scully,R., Livingston,D.M., Li,L., Blackwell,C.B., Futreal,P.A. and Afshari,C.A. (2003) Novel consensus DNA-binding sequence for BRCA1 protein complexes. Mol. Carcinog., 38, 85-96. (Pubitemid 37255144)
46. Orlov,S.V., Kuteykin-Teplyakov,K.B., Ignatovich,I.A., Dizhe,E.B., Mirgorodskaya,O.A., Grishin,A.V., Guzhova,O.B., Prokhortchouk,E.B., Guliy,P.V. and Perevozchikov,A.P. (2007) Novel repressor of the human FMR1 gene - identification of p56 human (GCC)(n)-binding protein as a Kruppel-like transcription factor ZF5. FEBS J., 274, 4848-4862. (Pubitemid 47353130)
47. El-Tanani,M.K., Campbell,F.C., Crowe,P., Erwin,P., Harkin,D.P., Pharoah,P., Ponder,B. and Rudland,P.S. (2006) BRCA1 suppresses osteopontin-mediated breast cancer. J. Biol. Chem., 281, 26587-26601. (Pubitemid 44401868)
48. Stanescu,H., Wolfsberg,T.G., Moreland,R.T., Ayub,M.H., Erickson,E., Westbroek,W., Huizing,M., Gahl,W.A. and Helip-Wooley,A. (2009) Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting. Ann. Hum. Genet., 73, 422-428.
49. Cogswell,J.P., Godlevski,M.M., Bonham,M., Bisi,J. and Babiss,L. (1995) Upstream stimulatory factor regulates expression of the cell cycle-dependent cyclin B1 gene promoter. Mol Cell Biol., 15, 2782-2790.
50. Trembley,J.H., Chen,Z., Rodrigues,C.M., Kren,B.T., Steer,C.J. (2000) Genomic organization and promoter characterization of the rat cyclin B1 gene. Gene., 255, 93-104.
51. MacLachlan,T.K., Somasundaram,K., Sgagias,M., Shifman,Y., Muschel,R.J., Cowan,K.H. and El-Deiry,W.S. (2000) BRCA1 effects on the cell cycle and the DNA damage response are linked to altered gene expression. J. Biol. Chem., 275, 2777-2785. (Pubitemid 30082049)