A common cis-element in promoters of protein synthesis and cell cycle genes

• Authors: Lucjan S Wyrwicz , Paweł Gaj , Marcin Hoffmann , Leszek Rychlewski , Jerzy Ostrowski
• Languages of publication: EN

Abstracts

EN

Gene promoters contain several classes of functional sequence elements (cis elements) recognized by protein agents, e.g. transcription factors and essential components of the transcription machinery. Here we describe a common DNA regulatory element (tandem TCTCGCGAGA motif) of human TATA-less promoters. A combination of bioinformatic and experimental methodology suggests that the element can be critical for expression of genes involved in enhanced protein synthesis and the G1/S transition in the cell cycle. The motif was identified in a substantial fraction of promoters of cell cycle genes, like cyclins (CCNC, CCNG1), as well as transcription regulators (TAF7, TAF13, KLF7, NCOA2), chromatin structure modulators (HDAC2, TAF6L), translation initiation factors (EIF5, EIF2S1, EIF4G2, EIF3S8, EIF4) and previously reported 18 ribosomal protein genes. Since the motif can define a subset of promoters with a distinct mechanism of activation involved in regulation of expression of about 5% of human genes, further investigation of this regulatory element is an emerging task.

Keywords

EN

gel shift assay; regulation of transcription; comparative genomics; gene expression; promoter; bioinformatics

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2007
• Volume: 54
• Issue: 1
• Pages: 89-98

Dates

published

2007

received

2006-11-28

revised

2007-02-13

accepted

2007-02-16

(unknown)

2007-03-09

Contributors

author

Lucjan S Wyrwicz

• BioInfoBank Institute, Poznań, Poland

author

Paweł Gaj

• Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warszawa, Poland

author

Marcin Hoffmann

• BioInfoBank Institute, Poznań, Poland

author

Leszek Rychlewski

• BioInfoBank Institute, Poznań, Poland

author

Jerzy Ostrowski

• Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warszawa, Poland

References

• Bairoch A, Apweiler R et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res 33: D154-159.
• Barrera L, Ren B (2006) The transcriptional regulatory code of eukaryotic cells-insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol 18: 291-298.
• Edgar R, Domrachev M, Lash A (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acid Res 30: 207-210.
• Feller W (1968) An introduction to probability theory and its applications. Vol 1, 3rd edn, Wiley.
• FitzGerald P, Shlyakhtenko A, Mir A, Vinson C (2004) Clustering of DNA sequences in human promoters. Genome Res 14: 1562-1574.
• Frech K, Quandt K, Werner T (1998) Muscle actin genes: a first step towards computational classification of tissue specific promoters. In Silico Biol 1: 29-38.
• Gniazdowski M, Czyz M (1999) Transcription factors as targets of anticancer drugs. Acta Biochim Polon 46: 255-262.
• Hardison R, Slightom J, Gumucio D, Goodman M, Stojanovic N, Miller W (1997) Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205: 73-94.
• Harris M, Clark J et al. (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261.
• Haun R, Moss J, Vaughan M (1993) Characterization of the human ADP-ribosylation factor 3 promoter transcriptional regulation of a TATA-less promoter. J Biol Chem 268: 8793-8800.
• Hoh J, Jin S, Parrado T, Edington J, Levine A, Ott J (2002) The p53MH algorithm and its application in detecting p53-responsive genes. Proc Natl Acad Sci USA 99: 8467-8472.
• Hughes J, Estep P, Tavazoie S, Church G (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296: 1205-1214.
• Jura J, Wegrzyn P, Jura J, Koj A (2006) Regulatory mechanisms of gene expression: complexity with elements of deterministic chaos. Acta Biochim Polon 53: 1-10.
• Kel A, Kel-Margoulis O, Farnham P, Bartley S, Wingender E, Zhang M (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. J Mol Biol 309: 99-120.
• Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A, Haussler D (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
• Klimek-Tomczak K, Wyrwicz L, Jain S, Bomsztyk K, Ostrowski J (2004) Characterization of hnRNP K protein-RNA interactions. J Mol Biol 342: 1131-1141.
• Kozak M (1987) An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15: 8125-8148.
• Makalowski W (2001) The human genome structure and organization. Acta Biochim Polon 48: 587-598.
• Ostrowski J, Sims J, Sibley C, Valentine M, Dower S, Meier K, Bomsztyk K (1991) A serine/threonine kinase activity is closely associated with a 65-kDa phosphoprotein specifically recognized by the kB enhancer element. J Biol Chem 266: 12722-12733.
• Pennacchio L, Rubin E (2001) Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2: 100-109.
• Perry R (2005) The architecture of mammalian ribosomal protein promoters. BMC Evol Biol 5: 15.
• Roepcke S, Zhi D, Vingron M, Arndt P (2006) Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters. Gene 365: 48-56.
• Schmid C, Périer R, Praz V, Bucher P (2006) EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res 34: D82-D85.
• Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
• Segal E, Friedman N, Koller D, Regev A (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36: 1090-1098.
• Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 266: 231-245.
• van Ruissen F, Ruijter J, Schaaf G, Asgharnegad L, Zwijnenburg D, Kool M, Baas F (2005) Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics 6: 91.
• Velculescu V, Zhang L, Vogelstein B, Kinzler K (1995) Serial analysis of gene expression. Science 270: 484-487.
• Wasserman W, Fickett J (1998) Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 278: 167-181.
• Xie X, Lu J, Kulbokas E, Golub T, Mootha V, Lindblad-Toh K, Lander E, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434: 338-345.
• Yoshihama M, Uechi T et al. (2002) The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res 12: 379-390.