Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes

PLoS Computational Biology

Volumn 3, Issue 4, 2007, Pages 733-742

  Yang, Mary Q ^a   Koehly, Laura M ^a   Elnitski, Laura L ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; TRANSCRIPTION;

BREAST CANCER; CANCER GENES; CO-REGULATION; DNA-REPAIR; EXPRESSED SEQUENCE TAGS; HUMAN GENOMES; HUMAN TRANSCRIPTS; OVARIAN CANCERS; REGULATORY REGIONS; TRANSCRIPTION START SITE;

DISEASES;

BRCA2 PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FANCONI ANEMIA GROUP D2 PROTEIN; TRANSCRIPTION FACTOR; TUMOR MARKER; TUMOR PROTEIN;

ARTICLE; BINDING SITE; BREAST CANCER; CONTROLLED STUDY; DNA REPAIR; EXPRESSED SEQUENCE TAG; GENE CONTROL; GENE FUNCTION; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; OVARY CANCER; TUMOR GENE; BREAST TUMOR; DNA SEQUENCE; FEMALE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETICS; INFORMATION RETRIEVAL; METHODOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; OVARY TUMOR; PROMOTER REGION; SEQUENCE ALIGNMENT;

BASE SEQUENCE; BREAST NEOPLASMS; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NEOPLASM PROTEINS; OVARIAN NEOPLASMS; PROMOTER REGIONS, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TUMOR MARKERS, BIOLOGICAL;

EID: 34247561298     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030072     Document Type: Article

References (32)

1. Adachi N, Lieber MR (2002) Bidirectional gene organization: A common architectural feature of the human genome. Cell 109: 807-809.
2. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, et al. (2004) An abundance of bidirectional promoters in the human genome. Genome Res 14: 62-66.
3. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex loci in human and mouse genomes. PLoS Genet 2: e47.
4. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72: 449-479.
5. Yamashita R, Suzuki Y, Wakaguri H, Tsuritani K, Nakai K, et al. (2006) DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res 34: D86-D89.
6. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2006) GenBank. Nucleic Acids Res 34: D16-D20.
7. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, et al. (2005) A high-resolution map of active promoters in the human genome. Nature 436: 876-880.
8. Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, et al. (2006) CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis. Nucleic Acids Res 34: D632-D636.
9. Forbes S, Clements J, Dawson E, Bamford S, Webb T, et al. (2006) COSMIC 2005. Br J Cancer 94: 318-322.
10. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, et al. (2006) The consensus coding sequences of human breast and colorectal cancers. Science 314: 268-274.
11. Hecht JL, Mutter GL (2006) Molecular and pathologic aspects of endometrial carcinogenesis. J Clin Oncol 24: 4783-4791.
12. Xu CF, Brown MA, Nicolai H, Chambers JA, Griffiths BL, et al. (1997) Isolation and characterisation of the NBR2 gene which lies head to head with the human BRCA1 gene. Hum Mol Genet 6: 1057-1062.
13. Wei C, Brent MR (2006) Integrating EST alignments and de novo gene prediction using TWINSCAN. BMC Bioinformatics 7: 327.
14. Consortium GO (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34: D322-D326.
15. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
16. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
17. Campan M, Weisenberger DJ, Laird PW (2006) DNA methylation profiles of female steroid hormone-driven human malignancies. Curr Top Microbiol Immunol 310: 141-178.
18. Li D, Das S, Yamada T, Samuels HH (2004) The NRIF3 family of transcriptional coregulators induces rapid and profound apoptosis in breast cancer cells. Mol Cell Biol 24: 3838-3848.
19. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
20. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
21. Hsu T, Trojanowska M, Watson DK (2004) Ets proteins in biological control and cancer. J Cell Biochem 91: 896-903.
22. Barthel R, Tsytsykova AV, Barczak AK, Tsai EY, Dascher CC, et al. (2003) Regulation of tumor necrosis factor alpha gene expression by mycobacteria involves the assembly of a unique enhanceosome dependent on the coactivator proteins CBP/p300. Mol Cell Biol 23: 526-533.
23. Hitchins M, Williams R, Cheong K, Halani N, Lin VA, et al. (2005) MLH1 germline epimutations as a factor in hereditary nonpolyposis colorectal cancer. Gastroenterology 129: 1392-1399.
24. Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, et al. (2006) CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 38: 787-793.
25. Shu J, Jelinek J, Chang H, Shen L, Qin T, et al. (2006) Silencing of bidirectional promoters by DNA methylation in tumorigenesis. Cancer Res 66: 5077-5084.
26. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, et al. (2006) The UCSC known genes. Bioinformatics 22: 1036-1046.
27. Beissbarth T, Speed TP (2004) GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.
28. Wilcox CB, Baysal BE, Gallion HH, Strange MA, DeLoia JA (2005) High-resolution methylation analysis of the BRCA1 promoter in ovarian tumors. Cancer Genet Cytogenet 159: 114-122.
29. Dhillon VS, Shahid M, Husain SA (2004) CpG methylation of the FHIT, FANCF, cyclin-D2, BRCA2 and RUNX3 genes in Granulosa cell tumors (GCTs) of ovarian origin. Mol Cancer 3: 33.
30. Zhang P, Wang J, Gao W, Yuan BZ, Rogers J, et al. (2004) CHK2 kinase expression is down-regulated due to promoter methylation in non-small cell lung cancer. Mol Cancer 3: 14.
31. Fiegl H, Millinger S, Goebel G, Muller-Holzner E, Marth C, et al. (2006) Breast cancer DNA methylation profiles in cancer cells and tumor stroma: Association with HER-2/neu status in primary breast cancer. Cancer Res 66: 29-33.
32. Amatya VJ, Naumann U, Weller M, Ohgaki H (2005) TP53 promoter methylation in human gliomas. Acta Neuropathol (Berlin) 110: 178-184.