Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22

References

• Alberts GF, Peifley KA, Johns A, Kleha JF, Winkles JA. Constitutive endothelin-1 overexpression promotes smooth muscle cell proliferation via an external autocrine loop. J Biol Chem 1994; 269: 10112–10118
   PubMed Web of Science ®Google Scholar
• Alberts B, Johnson A, Lewis J, Raff MK, Roberts K, Walter P. Molecular biology of the cell. Garland Science, New York 2002
   Google Scholar
• Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinform 2004; 5: 18
   PubMed Web of Science ®Google Scholar
• Antequera F, Bird A. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 1993; 90: 11995–11999
   PubMed Web of Science ®Google Scholar
• Arkhipova IR. Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics 1995; 139: 1359–1369
   PubMedGoogle Scholar
• Berk AJ. Activation of RNA polymerase II transcription. Curr Opin Cell Biol 1999; 11: 330–335
   PubMedGoogle Scholar
• Blake M, Niklinski J, Zajac-Kaye M. Interactions of the transcription factors MIBP1 and RFX1 with the EP element of the hepatitis B virus enhancer. J Virol 1996; 70: 6060–6066
   Google Scholar
• Breathnach R, Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 1981; 50: 349–383
   PubMed Web of Science ®Google Scholar
• Burke TW, Kadonaga JT. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 1997; 11: 3020–3031
   PubMed Web of Science ®Google Scholar
• Butchbach ME, Lai L, Lin CL. Molecular cloning, gene structure, expression profile and functional characterization of the mouse glutamate transporter (EAAT3) interacting protein GTRAP3-18. Gene 2002; 292: 81–90
   PubMed Web of Science ®Google Scholar
• Butler JE, Kadonaga JT. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 2001; 15: 2515–2519
   PubMed Web of Science ®Google Scholar
• Butler JE, Kadonaga JT. The RNA polymerase II core promoter: A key component in the regulation of gene expression. Genes Dev 2002; 16: 2583–2592
   PubMed Web of Science ®Google Scholar
• Carroll JD, Wallace RC, Keane J, Remold HG, Arbeit RD. Identification of Mycobacterium avium DNA sequences that encode exported proteins by using phoA gene fusions. Tuber Lung Dis 2000; 80: 117–130
   Google Scholar
• Chen C, Gentles AJ, Jurka J, Karlin S. Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002; 99: 2930–2935
   Google Scholar
• Clegg CH, Haugen HS, Boring LF. Promoter sequences in the RI beta subunit gene of cAMP-dependent protein kinase required for transgene expression in mouse brain. J Biol Chem 1996; 271: 1638–1644
   Google Scholar
• Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001; 29: 412–417
   PubMedGoogle Scholar
• Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002; 12: 458–461
   PubMed Web of Science ®Google Scholar
• Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998; 95: 14863–14868
   PubMed Web of Science ®Google Scholar
• Featherstone M. Coactivators in transcription initiation: Here are your orders. Curr Opin Genet Dev 2002; 12: 149–155
   PubMedGoogle Scholar
• Fessele S, Maier H, Zischek C, Nelson PJ, Werner T. Regulatory context is a crucial part of gene function. Trends Genet 2002; 18: 60–63
   PubMed Web of Science ®Google Scholar
• Fickett JW, Hatzigeorgiou AG. Eukaryotic promoter recognition. Genome Res 1997; 7: 861–878
   PubMedGoogle Scholar
• Fickett JW, Wasserman WW. Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol 2000; 11: 19–24
   PubMed Web of Science ®Google Scholar
• Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196: 261–282
   PubMed Web of Science ®Google Scholar
• Gershenzon NI, Ioshikhes IP. Promoter classifier: Software package for promoter database analysis. Appl Bioinformatics 2005; 4: 205–209
   Google Scholar
• Goldberg ML. 1979. PhD Thesis. Stanford University.
   Google Scholar
• Gowik U, Burscheidt J, Akyildiz M, Schlue U, Koczor M, Streubel M, Westhoff P. cis-Regulatory elements for mesophyll-specific gene expression in the C4 plant Flaveria trinervia, the promoter of the C4 phosphoenolpyruvate carboxylase gene. Plant Cell 2004; 16: 1077–1090
   Google Scholar
• Huang EY, Madireddi MT, Gopalkrishnan RV, Leszczyniecka M, Su Z, Lebedeva IV, Kang D, Jiang H, Lin JJ, Alexandre D, et al. Genomic structure, chromosomal localization and expression profile of a novel melanoma differentiation associated (mda-7) gene with cancer specific growth suppressing and apoptosis inducing properties. Oncogene 2001; 20: 7051–7063
   PubMed Web of Science ®Google Scholar
• Hultmark D, Klemenz R, Gehring WJ. Translational and transcriptional control elements in the untranslated leader of the heat-shock gene hsp22. Cell 1986; 44: 429–438
   PubMedGoogle Scholar
• Kadonaga JT. The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med 2002; 34: 259–264
   PubMedGoogle Scholar
• Kawai Y, Asai K, Miura Y, Inoue Y, Yamamoto M, Moriyama A, Yamamoto N, Kato T. Structure and promoter activity of the human glia maturation factor-gamma gene: A TATA-less, GC-rich and bidirectional promoter. Biochim Biophys Acta 2003; 1625: 246–252
   Google Scholar
• Kutach AK, Kadonaga JT. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol Cell Biol 2000; 20: 4754–4764
   PubMed Web of Science ®Google Scholar
• Lemercier C, Brown A, Mamani M, Ripoche J, Reiffers J. The rat Mist1 gene: Structure and promoter characterization. Gene 2000; 242: 209–218
   PubMedGoogle Scholar
• Li WH. Molecular evolution. Sinauer, Massachusetts 1997
   Google Scholar
• Liu GB, Yan H, Jiang YF, Chen R, Pettigrew JD, Zhao KN. The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes. Gene 2005; 358: 127–138
   Google Scholar
• Machida H, Ito M, Okamoto R, Shiraki K, Isaka N, Hartshorne DJ, Nakano T. Molecular cloning and analysis of the 5′-flanking region of the human MYPT1 gene. Biochim Biophys Acta 2001; 1517: 424–429
   Google Scholar
• Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res 2004; 32: 949–958
   PubMedGoogle Scholar
• Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc Natl Acad Sci USA 1996; 93: 4862–4867
   PubMedGoogle Scholar
• Nikolov DB, Burley SK. RNA polymerase II transcription initiation: A structural view. Proc Natl Acad Sci USA 1997; 94: 15–22
   PubMed Web of Science ®Google Scholar
• Ohler U, Liao GC, Niemann H, Rubin GM. Computational analysis of core promoters in the Drosophila genome. Genome Biol 2002; 3: RESEARCH0087
   PubMedGoogle Scholar
• Ohlsson R, Kanduri C. New twists on the epigenetics of CpG islands. Genome Res 2002; 12: 525–526
   Google Scholar
• Penalva MA, Arst HN, Jr. Recent advances in the characterization of ambient pH regulation of gene expression in filamentous fungi and yeasts. Annu Rev Microbiol 2004; 58: 425–451
   PubMed Web of Science ®Google Scholar
• Purnell BA, Emanuel PA, Gilmour DS. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes Dev 1994; 8: 830–842
   PubMedGoogle Scholar
• Roeder RG. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 1996a; 21: 327–335
   PubMed Web of Science ®Google Scholar
• Roeder RG. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 1996b; 21: 327–335
   PubMed Web of Science ®Google Scholar
• Shields DJ, Agellon LB, Vance DE. Structure, expression profile and alternative processing of the human phosphatidylethanolamine N-methyltransferase (PEMT) gene. Biochim Biophys Acta 2001; 1532: 105–114
   Google Scholar
• Shimada T, Fujii H, Lin H. A 165-base pair sequence between the dihydrofolate reductase gene and the divergently transcribed upstream gene is sufficient for bidirectional transcriptional activity. J Biol Chem 1989; 264: 20171–20174
   PubMedGoogle Scholar
• Smale ST, Baltimore D. The “initiator” as a transcription control element. Cell 1989; 57: 103–113
   PubMed Web of Science ®Google Scholar
• Smale ST. Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim Biophys Acta 1997; 1351: 73–88
   PubMedGoogle Scholar
• Smale ST, Jain A, Kaufmann J, Emami KH, Lo K, Garraway IP. The initiator element: A paradigm for core promoter heterogeneity within metazoan protein-coding genes. Cold Spring Harb Symp Quant Biol 1998; 63: 21–31
   PubMedGoogle Scholar
• Smale ST, Kadonaga JT. The RNA polymerase II core promoter. Annu Rev Biochem 2003; 72: 449–479
   PubMed Web of Science ®Google Scholar
• Stapleton T, Luchman A, Johnston J, Browder L, Brenner S, Venkatesh B, Jirik FR. Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: Characterization of Fugu 3′-phosphoadenosine 5′-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenic Xenopus. FEBS Lett 2004; 556: 59–63
   Google Scholar
• Streb JW, Kitchen CM, Gelman IH, Miano JM. Multiple promoters direct expression of three AKAP12 isoforms with distinct subcellular and tissue distribution profiles. J Biol Chem 2004; 279: 56014–56023
   Google Scholar
• Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, et al. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res 2001; 11: 677–684
   PubMedGoogle Scholar
• Suzuki F, Suzuki Y, Tsubota A, Akuta N, Someya T, Kobayashi M, Saitoh S, Arase Y, Ikeda K, Kumada H. Mutations of polymerase, precore and core promoter gene in hepatitis B virus during 5-year lamivudine therapy. J Hepatol 2002; 37: 824–830
   PubMed Web of Science ®Google Scholar
• Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002; 99: 3740–3745
   PubMed Web of Science ®Google Scholar
• Terai G, Takagi T. Predicting rules on organization of cis-regulatory elements, taking the order of elements into account. Bioinformatics 2004; 20: 1119–1128
   Google Scholar
• Tewari DS, Cook DM, Taub R. Characterization of the promoter region and 3′ end of the human insulin receptor gene. J Biol Chem 1989; 264: 16238–16245
   PubMedGoogle Scholar
• Tjian R, Maniatis T. Transcriptional activation: A complex puzzle with few easy pieces. Cell 1994; 77: 5–8
   PubMed Web of Science ®Google Scholar
• Trinklein ND, Aldred SJ, Saldanha AJ, Myers RM. Identification and functional analysis of human transcriptional promoters. Genome Res 2003; 13: 308–312
   Google Scholar
• Tye AJ, Ghebrehiwet B, Guo N, Sastry KN, Chow BK, Peerschke EI, Lim BL. The human gC1qR/p32 gene, C1qBP. Genomic organization and promoter analysis. J Biol Chem 2001; 276: 17069–17075
   Google Scholar
• Wang S, Wang W, Wesley RA, Danner RL. A Sp1 binding site of the tumor necrosis factor alpha promoter functions as a nitric oxide response element. J Biol Chem 1999; 274: 33190–33193
   PubMedGoogle Scholar
• Watari H, Blanchette-Mackie EJ, Dwyer NK, Watari M, Burd CG, Patel S, Pentchev PG, Strauss JF, 3rd. Determinants of NPC1 expression and action: Key promoter regions, posttranscriptional control, and the importance of a “cysteine-rich” loop. Exp Cell Res 2000; 259: 247–256
   PubMed Web of Science ®Google Scholar
• Zhou T, Chiang CM. Sp1 and AP2 regulate but do not constitute TATA-less human TAF(II)55 core promoter activity. Nucleic Acids Res 2002; 30: 4145–4157
   PubMedGoogle Scholar