Abstract
Eukaryotic gene expression is dependent on short protein-binding DNA sequence motifs promoting the assembly of multiprotein transcription complexes. Human retroposons of theAlu family are known to contain some high-affinity binding sites for transcription factors, which may serve as signals in regulation of expression of RNA-polymerase II-transcribed genes. In this computer study we have compared the density of ten consensus transcription factor binding sites in a set of human mature mRNA, human promotors andAlu repeats. Our results indicate thatAlu retroposons and promotor sequences have significantly higher mean density of these sites compared to RNAs. It is suggested that the majority ofAlu repeats do have the potential for regulating gene expression via modulation of RNA polymerase II-dependent transcription.
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References
Batzer, M.A. & P.L. Deininger, 1991. A human-specific subfamily of Alu sequences. Genomics 9: 481–487.
Bird, A., 1992. The essentials of DNA methylation. Cell 70: 5–8.
Bladon, T.S. & M.W. McBurney, 1991. The rodent B2 sequences can effect expression when present in the transcribed region of a reporter gene. Gene 98: 259–266.
Boulikas, T., 1994. A compliation and classification of DNA binding sites for protein transcription factors from vertebrates. Critical Reviews in Eukaryotic Gene Expression 4: 117–321.
Boyes, J. & A. Bird, 1992. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of methyl-CpG binding protein. EMBO J. 11: 327–333.
Brini, A.T., G.M. Lee & J.-P. Kinet, 1993. Involvement of Alu sequences in the cell-specific regulation of transcription of the g chain of Fe and T cell receptors. J. Biol. Chem. 269: 1335–1361.
Britten, R.J., 1994. Evolutionary selection against changes in many Alu repeats sequences interspersed through primate genomes. Proc. Natl. Acad. Sci. USA 91: 5992–5996.
Brosius, J., 1991. Retroposons — seeds of evolution. Science 251: 753.
Brosius, J. & S.J. Gould, 1992. On ‘genomenclature’: a comprehensive (and respectful) taxonomy for pseudogenes and other ‘Junk DNA’. Proc. Natl. Acad. Sci. USA 89: 10706–10710.
Chesnokov, I., V. Bozhkov, B. Popov & N. Tomilin, 1991. Binding specificity of human nuclear protein interacting with the Alu family DNA repeats. Biochem. Biophys. Res. Commun. 178: 613–619.
Culotta, V.C. & D.H. Hamer, 1989. Fine mapping of a mouse metallothionein gene metal response element. Mol. Cell. Biol. 9: 1376–1380.
Deininger, P.L. & M.A. Batzer, 1993. Evolution of retroposons, pp. 157–196 in Evolutionary Biology, volume 27, edited by Max K. Hecht et al. Plenum Press, New York.
Faisst, S. & S. Meyer, 1992. Compilation of vertebrate-encoded transcription factors. Nucl. Acids Res. 1: 3–26.
Hambor, J.E., J. Mennone, M.E. Coon, J.H. Hanke & P. Kavathas, 1993. Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8-alpha gene. Mol. Cell. Biol. 13: 7056–7070.
Joulin, V., D. Bories, J.-F. Eleouet, M.C. Labastie, S. Chreitien, M.-G. Mattei & P.-H. Romeo, 1991. A T-cell specific TCR delta DNA binding protein is a member of the human GATA family. EMBO J. 10: 1809–1816.
Jurka, J., 1993. A new subfamily of recently retroposed human Alu repeats. Nucl. Acids Res. 21: 2252.
Issemann, I. & S. Green, 1990. Activation of a member of the steroid hormone receptor superfamily by peroxisome proliferators. Nature 347: 645–650.
Kadonaga, J.T., K.R. Carner, F.R. Masiarz & R. Tijan, 1987. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell 51: 1079–1090.
Kidwell, M., 1992. Horizontal transfer. Curr. Opin. Genet. Devel. 2: 868–873.
Kim, J., C. Yu, A. Bailey, R. Hardison & C. Shen, 1989. Unique sequence organization of erythroid-specific nuclear factor-binding of mammalian theta-1-globin promoters. Nucl. Acids Res. 17: 5687–5701.
Kochanek, S., D. Renz & W. Doerfler, 1993. DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J. 12: 1141–1151.
Lambert, M.E., J.F. McDonald & I.B. Weinstein, 1989. Eukaryotic transposable elements as mutagenic agents. New York, Cold Spring Harbor Press.
Liu, W.-M., R.J. Maraia, C.M. Rubin & C.W. Schmid, 1994. Alu transcripts: cytoplasmic localization and regulation by DNA methylation. Nucl. Acids. Res. 22: 1087–1095.
Matera, A.G., U. Hellman & C.W. Schmid, 1990. A transpositionally and transcriptionally competent Alu subfamily. Mol. Cell. Biol. 10: 5424–5432.
McDonald, J.F., 1990. Macroevolution and retroviral elements. Bio-Science 40: 183–191.
McDonald, J.F., 1993. Evolution and consequences of transposable elements. Curr. Opin. Genet. Devel. 3: 855–864.
McKinnon, R.D., P. Danielson, M.A. Brow, M. Godbout, J.B. Watson & J.G. Sutcliffe, 1987. The neuronal identifier sequence is a positive regulatory element for neuronal gene expression, pp. 78–85, in From Message to Mind: Directions In Developmental Neurobiology, edited by S. Easter, K. Barald & B. Carlson, Sinauer, Sunderland, Massachusetts.
McKnight, S. & Y. Yamamoto (eds.), 1992. Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Oliviero, S. & P. Monaci, 1988. RNA polymerase III promoter elements enhance transcription of RNA polymerase III genes. Nucl. Acids. Res. 16: 1285–1293.
Prendergast, G.C. & E.B. Ziff, 1991. Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region. Science 251: 186–189.
Rorth, P., C. Nerlov, F. Blasi & M. Johnsen, 1990. Transcription factor PEA-3 participates in the induction of urokinase plasminogen activator transcription in murine keratinocytes stimulated with epidermal growth factor or phorbol ester. Nucl. Acids. Res. 18: 5009–5017.
Saegusa, Y., M. Sato, I. Galli, T. Nakagawa, N. Ono, S.M.M. Iguchi-Ariga & H. Ariga, 1993. Stimulation of DNA replication and transcription by Alu family sequence. Biochim. Biophys. Acta 1172: 274–282.
Saffer, J.D. & S.J. Thurston, 1989. A negative regulatory element with properties similar to those of enhancers is contained within an Alu sequence. Mol. Cell. Biol. 9: 355–364.
Schmid, C.W. 1991. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucl. Acids. Res. 19: 5613–5617.
Schmid, C.W. & R. Maraia, 1993. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Devel. 2: 874–882.
Stavenhagen, J. & D. Robins, 1988. An ancient provirus has imposed androgen regulation on the adjacent mouse sex-limited protein gene. Cell 55: 247–254.
Von Sternberg, R., G. Novick, G. Gao & R. Herrera, 1993. Genome canalization: the coevolution of transposable elements with single-copy DNA, pp. 108–139 in Transposable Elements and Evolution, edited by J.F. McDonald. Kluwer Academic Publishers, Dordrecht.
Tomilin, N. & V. Bozhkov, 1989. Human nuclear protein interacting with a conservative sequence motif of Alu-family DNA repeats. FEBS Letters 251: 79–83.
Tomilin, N., S. Iguchi-Ariga & H. Ariga, 1990. Transcription and replication silencer is present within conserved region of human Alu repeats interacting with nuclear protein. FEBS Letters 263: 69–72.
Tomilin, N.V., V.M. Bozhkov, E.M. Bradbury & C.W. Schmid, 1992. Differential binding of human nuclear proteins to Alu subfamilies. Nucl. Acids Res. 20: 2941–2945.
Wallace, M.R., L.B. Andersen, A.M. Saulino, P.E. Gregory, T.W. Glover & F.S. Collins, 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353: 864–867.
Wagner, B.J., T.E. Hayes, C.J. Hoban & B.H. Cochran, 1990. The SIF binding element confer sis/PDGF inducibility onto c-fos promoter. EMBO J. 9: 4477–4484.
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Kazakov, V.I., Tomilin, N.V. Increased concentration of some transcription factor binding sites in human retroposons of theAlu family. Genetica 97, 15–22 (1996). https://doi.org/10.1007/BF00132576
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DOI: https://doi.org/10.1007/BF00132576