Functional pleiotropy of an intramolecular triplex-forming fragment from the 3′-UTR of the rat Pigr gene

Physiological Genomics

Volumn 2001, Issue 5, 2001, Pages 53-65

  Fabregat, Isabel ^a   Koch, Katherine S ^b   Aoki, Takashi ^d   Atkinson, Allan E ^b   Dang, Huong ^b   Amosova, Olga ^e   Fresco, Jacques R ^e   Schildkraut, Carl L ^f   Leffert, Hyam L ^b,c  

^a Instituto de Bioquimica   (Spain)

^b San Diego   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d HEALTH SCIENCES UNIVERSITY OF HOKKAIDO   (Japan)

^e PRINCETON UNIVERSITY   (United States)

^f ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

d(GGA)n and d(GAA)n triplet repeats; Genome regulators; Polypurine polypyrimidine elements

Indexed keywords

MURINAE;

DNA; MICROSATELLITE DNA; SECRETORY COMPONENT; TRIPLEX DNA;

3' UNTRANSLATED REGION; ANIMAL; ANTIBODY SPECIFICITY; ARTICLE; CELL LINE; CHEMISTRY; CONFORMATION; DNA DENATURATION; DNA SUPERCOILING; ENHANCER REGION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLASMID; PROTEIN SYNTHESIS; RAT; REPORTER GENE; REPRODUCIBILITY; SPECIES DIFFERENCE; THERMODYNAMICS;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CELL LINE; DNA; DNA, SUPERHELICAL; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; GENES, REPORTER; HUMANS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; ORGAN SPECIFICITY; PLASMIDS; PROTEIN BIOSYNTHESIS; RATS; RECEPTORS, POLYMERIC IMMUNOGLOBULIN; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 0345876791     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.2001.5.2.53     Document Type: Article

References (66)

1. Aoki T, Koch KS, and Leffert HL. Attenuation of gene expression by a trinucleotide repeat-rich tract from the terminal exon of the rat hepatic polymeric immunoglobulin gene. J Mol Biol 267: 229-236, 1997.
2. Bates AD and Maxwell A. DNA Topology. Oxford, UK: IRL, 1993.
3. Bauer W and Vinograd J. The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. J Mol Biol 33: 141-171, 1968.
4. Bonilla PJ, Freytag SO, and Lutter C. Enhancer-activated plasmid transcription complexes contain constrained supercoiling. Nucleic Acids Res 19: 3965-3971, 1991.
5. Brabletz T, Jung A, Hlubek F, Lohberg C, Meiler J, Suchy U, and Kirchner T. Negative regulation of CD4 expression in T cells by the transcriptional repressor ZEB. Int Immunol 11: 1701-1708, 1999.
6. Chen AS, Reyes A, and Akeson R. A homopurine:homopyrimidine sequence derived from the rat neuronal cell adhesion molecule-encoding gene alters expression in transient transfections. Gene 128: 211-218, 1993.
7. Chou SH, Zhu L, and Reid BR. Sheared purine purine pairing in biology. J Mol Biol 267: 1055-1067, 1997.
8. Cozzarelli NR, Boles TC, and White JH. DNA Topology and Its Biological Effects. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1990, p. 139-184.
9. Crothers DM. Upsetting the balance of forces in DNA. Science 266: 1819-1820, 1994.
10. Davidson EH and Britten RJ. Regulation of gene expression: possible role of repetitive sequences. Science 204: 1052-1059, 1979.
11. Davis TL, Firulli AB, and Kinniburgh AJ. Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene. Proc Natl Acad Sci USA 86: 9682-9686, 1989.
12. Feo S, Antona V, Barbieri G, Passantino R, Cali L, and Giallongo A. Transcription of the human beta enolase gene (ENO-3) is regulated by an intronic muscle-specific enhancer that binds myocyte-specific enhancer factor 2 proteins and ubiquitous G-rich-box binding factors. Mol Cell Biol 15: 5991-6002, 1995.
13. Fernandes M, Xiao H, and Lis JT. Fine structure analyses of the Drosophila and Saccharomyces heat shock factor: heat shock element interactions. Nucleic Acids Res 22: 167-173, 1994.
14. Frank-Kamenetskii MD. DNA Topology and its Biological Effects. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1990, p. 185-216.
15. Frank-Kamenetskii MD and Mirkin SM. Triplex DNA structures. Annu Rev Biochem 64: 65-95, 1995.
16. Gautheret D, Major F, and Cedergren R. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets. J Mol Biol 229: 1049-1064, 1993.
17. Gee JE, Revankar GR, Rao TS, and Hogan ME. Triplex formation at the rat neu gene utilizing imidazole and 2′-deoxy-6-thioguanosine base substitutions. Biochemistry 34: 2042-2048, 1995.
18. Gilmour DS, Thomas GH, and Elgin SC. Drosophila nuclear proteins bind to regions of alternating C and T residues in gene promoters. Science 245: 1487-1490, 1989.
19. Grabczyk E and Fishman MC. A long purine-pyrimidine homopolymer acts as a transcriptional diode. J Biol Chem 270: 1791-1797, 1995.
20. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol 26: 365-369, 1967.
21. Howell R and Usdin K. The ability to form intrastrand tetraplexes is an evolutionarily conserved feature of the 3′ end of L1 retrotransposons. Mol Biol Evol 14: 144-155, 1997.
22. n repeats form intramolecular hairpins stabilized by different base-pairing interactions. Biochemistry 35: 13125-13135, 1996.
23. Huling S, Fournier GR, Feren A, Chuntharapai A, and Jones AL. Ontogeny of the secretory immune system: maturation of a functional pIg-R regulated by gene expression. Proc Natl Acad Sci USA 89: 4260-4264, 1992.
24. Johnson AC, Jinno Y, and Merlino GT. Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease. Mol Cell Biol 8: 4174-4184, 1988.
25. Johnson PH and Grossman LI. Electrophoresis of DNA in agarose gels. Optimizing separations of conformational isomers of double-and single-stranded DNA. Biochemistry 16: 4217-4225, 1977.
26. Klemsz MJ, McKercher SR, Celada A, Van Beveren C, and Maki RA. The macrophage and B cell-specific transcription factor PU.1 is related to the ets oncogene. Cell 61:113-124, 1990.
27. Koch K and Leffert HL. Growth control of differentiated fetal rat hepatocytes in primary monolayer culture. VI. Studies with conditioned medium and its functional interactions with serum factors. J Cell Biol 62: 780-791, 1974.
28. Koch KS, Fletcher RG, Grond M, Inyang AI, Lu XP, Brenner DA, and Leffert HL. Inactivation of plasmid reporter gene expression by one benzo(a)pyrene diol-epoxide DNA adduct in adult rat hepatocytes. Cancer Res 53: 2279-2286, 1993.
29. Koch KS, Fletcher RG, Grond M, and Leffert HL. A 43 bp cDNA sequence homology and triplet repeat motif among putative polymeric immunoglobulin receptor messenger RNAs in regenerating rat liver. Hepatology 18: 226-228, 1993.
30. Koch KS, Gleiberman AG, Aoki T, Leffert HL, Feren A, Jones AL, and Fodor EJ. Discordant expression and variable numbers of neighboring GGA-and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene. Nucleic Acids Res 23: 1098-1112, 1995.
31. Koch KS, Aoki T, Wang Y, Atkinson AE, Gleiberman AD, Glebov OK, and Leffert HL. Site-specific integration of targeted DNA into animal cell genomes. Gene 249: 135-144, 2000.
32. Krasilnikov AS, Panyutin IG, Samadashwily GM, Cox R, Lazurkin YS, and Mirkin SM. Mechanisms of triplex-caused polymerization arrest. Nucleic Acids Res 25: 1339-1346, 1997.
33. Krowczynska AM, Rudders RA, and Krontiris TG. The human minisatellite consensus at breakpoints of oncogene translocations. Nucleic Acids Res 18: 1121-1127, 1990.
34. Kushiro A and Sato T. Polymeric immunoglobulin gene of mouse: sequence, structure and chromosomal location. Gene 204: 277-282, 1997.
35. Lavelle L and Fresco JR. UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C(+)-T)6:[d(A-G)6.d(C-T)6]; evidence for a proton switch. Nucleic Acids Res 23: 2692-2705, 1995.
36. Leffert HL and Paul D. Studies on primary cultures of differentiated fetal liver cells. J Cell Biol 52: 559-568, 1972.
37. Leffert HL. Growth control of differentiated fetal rat hepatocytes in primary monolayer culture. V. Occurrence in dialyzed fetal bovine serum of macro-molecules having both positive and negative growth regulatory functions. J Cell Biol 62: 767-779, 1974.
38. Liu LF and Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84: 7024-7027, 1987.
39. Lu Q, Wallrath LL, Granok H, and Elgin SC. (CT)n(GA)n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Mol Cell Biol 13: 2802-2814, 1993.
40. Mariappan SVS, Catasti P, Silks LA III, Bradbury EM, and Gupta G. The high-resolution structure of the triplex formed by the GAA/TTC triplet repeat associated with Friedreich's ataxia. J Mol Biol 285: 2035-2052, 1999.
41. Martin JD, King DM, Slauch JM, and Frisque RJ. Differences in regulatory sequences of naturally occurring JC virus variants. J Virol 53: 306-311, 1985.
42. Maueler W, Kyas A, Keyl HG, and Epplen JT. A genome-derived (gaa.ttc)24 trinucleotide block binds nuclear protein(s) specifically and forms triple helices. Gene 215: 389-403, 1998.
43. Mendez E, Rocher A, Calero M, Girbes T, Citores L, and Soriano F. Primary structure of omega-hordothionin, a member of a novel family of thionins from barley endosperm, and its inhibition of protein synthesis in eukaryotic and prokaryotic cell-free systems. Eur J Biochem 239: 67-73, 1996.
44. Mirkin SM and Frank-Kamenetskii MD. H-DNA and related structures. Annu Rev Biophys Biomol Struct 23: 541-576, 1994.
45. Mizuguchi G, Kanei-Ishii C, Sawazaki T, Horikoshi M, Roeder RG, Yamamoto T, and Ishii S. Independent control of transcription initiations from two sites by an initiator-like element and TATA box in the human c-erbB-2 promoter. FEBS Lett 348: 80-88, 1994.
46. Molkentin JD, Jobe SM, and Markham BE. Alpha-myosin heavy chain gene regulation: delineation and characterization of the cardiac muscle-specific enhancer and muscle-specific promoter. J Mol Cell Cardiol 28: 1211-1225, 1996.
47. Ohshima K, Kang S, Larson JE, and Wells RD. Cloning, characterization, and properties of seven triplet repeat sequences. J Biol Chem 271: 16773-16783, 1996.
48. Ohshima K, Montermini L, Wells RD, and Pandolfo M. Inhibitory effects of expanded GAA TTC triplet repeats from intron I of the Friedreich ataxia gene on transcription and replication in vivo. J Biol Chem 273: 14588-14595, 1998.
49. Palla F, Melfi R, Anello L, Di Bernardo M, and Spinelli G. Enhancer blocking activity located near the 3′ end of the sea urchin early H2A histone gene. Proc Natl Acad Sci USA 94: 2272-2277, 1997.
50. Paul C, Simar-Blanchet AE, Ro HS, and Le Cam A. Characterization of three transcriptional repressor sites within the 3′ untranslated region of the rat serine protease inhibitor 23 gene. Eur J Biochem 254: 538-546, 1998.
51. Pina B, Hache RJ, Arnemann J, Chalepakis G, Slater EP, and Beato M. Hormonal induction of transfected genes depends on DNA topology. Mol Cell Biol 10: 625-633, 1990.
52. Prestridge DS. SIGNAL SCAN: a computer program that scans DNA sequences for eucaryotic transcription elements. Comput Appl Biosci 7: 203-206, 1991.
53. Reaban ME and Griffin JA. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature 348: 342-344, 1990.
54. Rippe RA, Brenner DA, and Leffert HL. DNA-mediated gene transfer into adult rat hepatocytes in primary culture. Mol Cell Biol 10: 689-695, 1990.
55. Rippe RA, Umezawa A, Kimball JP, Breindl M, and Brenner DA. Binding of upstream stimulatory factor to an E-box in the 3′-flanking region stimulates alpha1(I) collagen gene transcription. J Biol Chem 272: 1753-1760, 1997.
56. Ruediger R and Walter G. Quantitation of luciferase reporter mRNA by in vitro translation of total cellular RNA is faster and more sensitive than northern blotting and primer extension. Anal Biochem 253: 267-269, 1997.
57. San Miguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, and Bennetzen JL. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768, 1996.
58. Suda T, Mishima Y, Takayanagi K, Asakura H, Odani S, and Kominami R. A novel activity of HMG domains: promotion of the triple-stranded complex formation between DNA containing (GGA/TCC)11 and d(GGA)11 oligonucleotides. Nucleic Acids Res 24: 4733-4740, 1996.
59. Sutherland GR and Richards RI. Simple tandem DNA repeats and human genetic disease. Proc Natl Acad Sci USA 92: 3636-3641, 1995.
60. Tacke R, Tohyama M, Ogawa S, and Manley JL. Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing. Cell 93: 139-148, 1998.
61. Tanaka K, Watakabe A, and Shimura Y. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol Cell Biol 14: 1347-1354, 1994.
62. Weintraub H, Cheng PF, and Conrad K. Expression of transfected DNA depends on DNA topology. Cell 46: 115-122, 1986.
63. Weitzmann MN, Woodford KJ, and Usdin K. The development and use of a DNA polymerase arrest assay for the evaluation of parameters affecting intrastrand tetraplex formation. J Biol Chem 271: 20598-20964, 1996.
64. Wells RD and Warren ST. Genetic Instabilities and Hereditary Neurological Diseases. San Diego, CA: Academic, 1998.
65. Xie TD, Sun L, Zhao HG, Fuchs JA, and Tsong TY. Study of mechanisms of electric field-induced DNA transfection. IV. Effects of DNA topology on cell uptake and transfection efficiency. Biophys J 63: 1026-1031, 1992.
66. Xu G and Goodridge AG. Function of a C-rich sequence in the polypyrimidine/polypurine tract of the promoter of the chicken malic enzyme gene depends on promoter context. Arch Biochem Biophys 363: 202-212, 1999.