Short, interspersed repetitive DNA sequences in prokaryotic genomes (original) (raw)

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Selected References

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  1. Blackburn E. H. Telomeres: structure and synthesis. J Biol Chem. 1990 Apr 15;265(11):5919–5921. [PubMed] [Google Scholar]
  2. Britten R. J., Kohne D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968 Aug 9;161(3841):529–540. doi: 10.1126/science.161.3841.529. [DOI] [PubMed] [Google Scholar]
  3. Colman S. D., Hu P. C., Bott K. F. Prevalence of novel repeat sequences in and around the P1 operon in the genome of Mycoplasma pneumoniae. Gene. 1990 Mar 1;87(1):91–96. doi: 10.1016/0378-1119(90)90498-g. [DOI] [PubMed] [Google Scholar]
  4. Correia F. F., Inouye S., Inouye M. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA. J Bacteriol. 1986 Sep;167(3):1009–1015. doi: 10.1128/jb.167.3.1009-1015.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dahl M. K., Francoz E., Saurin W., Boos W., Manson M. D., Hofnung M. Comparison of sequences from the malB regions of Salmonella typhimurium and Enterobacter aerogenes with Escherichia coli K12: a potential new regulatory site in the interoperonic region. Mol Gen Genet. 1989 Aug;218(2):199–207. doi: 10.1007/BF00331269. [DOI] [PubMed] [Google Scholar]
  6. Dimri G. P., Rudd K. E., Morgan M. K., Bayat H., Ames G. F. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J Bacteriol. 1992 Jul;174(14):4583–4593. doi: 10.1128/jb.174.14.4583-4593.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Edwards A., Civitello A., Hammond H. A., Caskey C. T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 1991 Oct;49(4):746–756. [PMC free article] [PubMed] [Google Scholar]
  8. Eisenach K. D., Cave M. D., Bates J. H., Crawford J. T. Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J Infect Dis. 1990 May;161(5):977–981. doi: 10.1093/infdis/161.5.977. [DOI] [PubMed] [Google Scholar]
  9. Flores M., González V., Brom S., Martínez E., Piñero D., Romero D., Dávila G., Palacios R. Reiterated DNA sequences in Rhizobium and Agrobacterium spp. J Bacteriol. 1987 Dec;169(12):5782–5788. doi: 10.1128/jb.169.12.5782-5788.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fujitani S., Komano T., Inouye S. A unique repetitive DNA sequence in the Myxococcus xanthus genome. J Bacteriol. 1991 Mar;173(6):2125–2127. doi: 10.1128/jb.173.6.2125-2127.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gilson E., Bachellier S., Perrin S., Perrin D., Grimont P. A., Grimont F., Hofnung M. Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriaceae. Res Microbiol. 1990 Nov-Dec;141(9):1103–1116. doi: 10.1016/0923-2508(90)90084-4. [DOI] [PubMed] [Google Scholar]
  12. Gilson E., Clément J. M., Brutlag D., Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. doi: 10.1002/j.1460-2075.1984.tb01986.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gilson E., Perrin D., Clement J. M., Szmelcman S., Dassa E., Hofnung M. Palindromic units from E. coli as binding sites for a chromoid-associated protein. FEBS Lett. 1986 Oct 6;206(2):323–328. doi: 10.1016/0014-5793(86)81005-5. [DOI] [PubMed] [Google Scholar]
  14. Gilson E., Perrin D., Hofnung M. DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res. 1990 Jul 11;18(13):3941–3952. doi: 10.1093/nar/18.13.3941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gilson E., Rousset J. P., Clément J. M., Hofnung M. A subfamily of E. coli palindromic units implicated in transcription termination? Ann Inst Pasteur Microbiol. 1986 Nov-Dec;137B(3):259–270. doi: 10.1016/s0769-2609(86)80116-8. [DOI] [PubMed] [Google Scholar]
  16. Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 1991 Apr 11;19(7):1375–1383. doi: 10.1093/nar/19.7.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. The BIME family of bacterial highly repetitive sequences. Res Microbiol. 1991 Feb-Apr;142(2-3):217–222. doi: 10.1016/0923-2508(91)90033-7. [DOI] [PubMed] [Google Scholar]
  18. Glare E. M., Paton J. C., Premier R. R., Lawrence A. J., Nisbet I. T. Analysis of a repetitive DNA sequence from Bordetella pertussis and its application to the diagnosis of pertussis using the polymerase chain reaction. J Clin Microbiol. 1990 Sep;28(9):1982–1987. doi: 10.1128/jcm.28.9.1982-1987.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Guzzetta V., Montes de Oca-Luna R., Lupski J. R., Patel P. I. Isolation of region-specific and polymorphic markers from chromosome 17 by restricted Alu polymerase chain reaction. Genomics. 1991 Jan;9(1):31–36. doi: 10.1016/0888-7543(91)90217-3. [DOI] [PubMed] [Google Scholar]
  20. Haas R., Meyer T. F. The repertoire of silent pilus genes in Neisseria gonorrhoeae: evidence for gene conversion. Cell. 1986 Jan 17;44(1):107–115. doi: 10.1016/0092-8674(86)90489-7. [DOI] [PubMed] [Google Scholar]
  21. Halling S. M., Zehr E. S. Polymorphism in Brucella spp. due to highly repeated DNA. J Bacteriol. 1990 Dec;172(12):6637–6640. doi: 10.1128/jb.172.12.6637-6640.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Herman G. E., Nadeau J. H., Hardies S. C. Dispersed repetitive elements in mouse genome analysis. Mamm Genome. 1992;2(4):207–214. doi: 10.1007/BF00355430. [DOI] [PubMed] [Google Scholar]
  23. Higgins C. F., Ames G. F., Barnes W. M., Clement J. M., Hofnung M. A novel intercistronic regulatory element of prokaryotic operons. Nature. 1982 Aug 19;298(5876):760–762. doi: 10.1038/298760a0. [DOI] [PubMed] [Google Scholar]
  24. Higgins C. F., McLaren R. S., Newbury S. F. Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. Gene. 1988 Dec 10;72(1-2):3–14. doi: 10.1016/0378-1119(88)90122-9. [DOI] [PubMed] [Google Scholar]
  25. Hudson G. S., Davidson B. E. Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12. J Mol Biol. 1984 Dec 25;180(4):1023–1051. doi: 10.1016/0022-2836(84)90269-9. [DOI] [PubMed] [Google Scholar]
  26. Hulton C. S., Higgins C. F., Sharp P. M. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol. 1991 Apr;5(4):825–834. doi: 10.1111/j.1365-2958.1991.tb00755.x. [DOI] [PubMed] [Google Scholar]
  27. Jeffreys A. J., Wilson V., Thein S. L. Hypervariable 'minisatellite' regions in human DNA. Nature. 1985 Mar 7;314(6006):67–73. doi: 10.1038/314067a0. [DOI] [PubMed] [Google Scholar]
  28. Jelinek W. R., Toomey T. P., Leinwand L., Duncan C. H., Biro P. A., Choudary P. V., Weissman S. M., Rubin C. M., Houck C. M., Deininger P. L. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1398–1402. doi: 10.1073/pnas.77.3.1398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  30. Lennon E., Gutman P. D., Yao H. L., Minton K. W. A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK. J Bacteriol. 1991 Mar;173(6):2137–2140. doi: 10.1128/jb.173.6.2137-2140.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lin R. J., Capage M., Hill C. W. A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome. J Mol Biol. 1984 Jul 25;177(1):1–18. doi: 10.1016/0022-2836(84)90054-8. [DOI] [PubMed] [Google Scholar]
  32. Litt M., Luty J. A. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989 Mar;44(3):397–401. [PMC free article] [PubMed] [Google Scholar]
  33. Makino K., Kim S. K., Shinagawa H., Amemura M., Nakata A. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J Bacteriol. 1991 Apr;173(8):2665–2672. doi: 10.1128/jb.173.8.2665-2672.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mazel D., Houmard J., Castets A. M., Tandeau de Marsac N. Highly repetitive DNA sequences in cyanobacterial genomes. J Bacteriol. 1990 May;172(5):2755–2761. doi: 10.1128/jb.172.5.2755-2761.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nakamura Y., Leppert M., O'Connell P., Wolff R., Holm T., Culver M., Martin C., Fujimoto E., Hoff M., Kumlin E. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science. 1987 Mar 27;235(4796):1616–1622. doi: 10.1126/science.3029872. [DOI] [PubMed] [Google Scholar]
  36. Nelson D. L., Ledbetter S. A., Corbo L., Victoria M. F., Ramírez-Solis R., Webster T. D., Ledbetter D. H., Caskey C. T. Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6686–6690. doi: 10.1073/pnas.86.17.6686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Neuer-Nitsche B., Lu X. N., Werner D. Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome. Nucleic Acids Res. 1988 Sep 12;16(17):8351–8360. doi: 10.1093/nar/16.17.8351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Newbury S. F., Smith N. H., Higgins C. F. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell. 1987 Dec 24;51(6):1131–1143. doi: 10.1016/0092-8674(87)90599-x. [DOI] [PubMed] [Google Scholar]
  39. Newbury S. F., Smith N. H., Robinson E. C., Hiles I. D., Higgins C. F. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell. 1987 Jan 30;48(2):297–310. doi: 10.1016/0092-8674(87)90433-8. [DOI] [PubMed] [Google Scholar]
  40. Noda A., Courtright J. B., Denor P. F., Webb G., Kohara Y., Ishihama A. Rapid identification of specific genes in E. coli by hybridization to membranes containing the ordered set of phage clones. Biotechniques. 1991 Apr;10(4):474, 476-7. [PubMed] [Google Scholar]
  41. Nur I., LeBlanc D. J., Tully J. G. Short, interspersed, and repetitive DNA sequences in Spiroplasma species. Plasmid. 1987 Mar;17(2):110–116. doi: 10.1016/0147-619x(87)90017-5. [DOI] [PubMed] [Google Scholar]
  42. Patel P. I., Garcia C., Montes de Oca-Luna R., Malamut R. I., Franco B., Slaugenhaupt S., Chakravarti A., Lupski J. R. Isolation of a marker linked to the Charcot-Marie-Tooth disease type IA gene by differential Alu-PCR of human chromosome 17-retaining hybrids. Am J Hum Genet. 1990 Dec;47(6):926–934. [PMC free article] [PubMed] [Google Scholar]
  43. Petes T. D., Hill C. W. Recombination between repeated genes in microorganisms. Annu Rev Genet. 1988;22:147–168. doi: 10.1146/annurev.ge.22.120188.001051. [DOI] [PubMed] [Google Scholar]
  44. Riley D. E., Samadpour M., Krieger J. N. Detection of variable DNA repeats in diverse eukaryotic microorganisms by a single set of polymerase chain reaction primers. J Clin Microbiol. 1991 Dec;29(12):2746–2751. doi: 10.1128/jcm.29.12.2746-2751.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Ross B. C., Raios K., Jackson K., Dwyer B. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J Clin Microbiol. 1992 Apr;30(4):942–946. doi: 10.1128/jcm.30.4.942-946.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Rudd K. E., Miller W., Werner C., Ostell J., Tolstoshev C., Satterfield S. G. Mapping sequenced E.coli genes by computer: software, strategies and examples. Nucleic Acids Res. 1991 Feb 11;19(3):637–647. doi: 10.1093/nar/19.3.637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Ruland K., Wenzel R., Herrmann R. Analysis of three different repeated DNA elements present in the P1 operon of Mycoplasma pneumoniae: size, number and distribution on the genome. Nucleic Acids Res. 1990 Nov 11;18(21):6311–6317. doi: 10.1093/nar/18.21.6311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Russell G. C., Mann N. H. Analysis of inverted repeat DNA in the genome of Rhodomicrobium vannielii. J Gen Microbiol. 1986 Feb;132(2):325–330. doi: 10.1099/00221287-132-2-325. [DOI] [PubMed] [Google Scholar]
  49. Sadosky A. B., Davidson A., Lin R. J., Hill C. W. rhs gene family of Escherichia coli K-12. J Bacteriol. 1989 Feb;171(2):636–642. doi: 10.1128/jb.171.2.636-642.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sadosky A. B., Gray J. A., Hill C. W. The RhsD-E subfamily of Escherichia coli K-12. Nucleic Acids Res. 1991 Dec;19(25):7177–7183. doi: 10.1093/nar/19.25.7177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Sapienza C., Doolittle W. F. Unusual physical organization of the Halobacterium genome. Nature. 1982 Feb 4;295(5848):384–389. doi: 10.1038/295384a0. [DOI] [PubMed] [Google Scholar]
  52. Scherer S., Stevens D. A. A Candida albicans dispersed, repeated gene family and its epidemiologic applications. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1452–1456. doi: 10.1073/pnas.85.5.1452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Schmid C. W., Jelinek W. R. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. doi: 10.1126/science.6281889. [DOI] [PubMed] [Google Scholar]
  54. Sharples G. J., Lloyd R. G. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 1990 Nov 25;18(22):6503–6508. doi: 10.1093/nar/18.22.6503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Shyamala V., Schneider E., Ames G. F. Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point. EMBO J. 1990 Mar;9(3):939–946. doi: 10.1002/j.1460-2075.1990.tb08192.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Stern M. J., Ames G. F., Smith N. H., Robinson E. C., Higgins C. F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. doi: 10.1016/0092-8674(84)90436-7. [DOI] [PubMed] [Google Scholar]
  57. Stern M. J., Prossnitz E., Ames G. F. Role of the intercistronic region in post-transcriptional control of gene expression in the histidine transport operon of Salmonella typhimurium: involvement of REP sequences. Mol Microbiol. 1988 Jan;2(1):141–152. doi: 10.1111/j.1365-2958.1988.tb00015.x. [DOI] [PubMed] [Google Scholar]
  58. Stringer S. L., Hong S. T., Giuntoli D., Stringer J. R. Repeated DNA in Pneumocystis carinii. J Clin Microbiol. 1991 Jun;29(6):1194–1201. doi: 10.1128/jcm.29.6.1194-1201.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Su C. J., Chavoya A., Baseman J. B. Regions of Mycoplasma pneumoniae cytadhesin P1 structural gene exist as multiple copies. Infect Immun. 1988 Dec;56(12):3157–3161. doi: 10.1128/iai.56.12.3157-3161.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Subramanian P. S., Versalovic J., McCabe E. R., Lupski J. R. Rapid mapping of Escherichia coli::Tn5 insertion mutations by REP-Tn5 PCR. PCR Methods Appl. 1992 Feb;1(3):187–192. doi: 10.1101/gr.1.3.187. [DOI] [PubMed] [Google Scholar]
  61. Versalovic J., Koeuth T., Lupski J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991 Dec 25;19(24):6823–6831. doi: 10.1093/nar/19.24.6823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Weber J. L., May P. E. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 1989 Mar;44(3):388–396. [PMC free article] [PubMed] [Google Scholar]
  63. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. doi: 10.1093/nar/18.24.7213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Welsh J., McClelland M. Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Res. 1991 Oct 11;19(19):5275–5279. doi: 10.1093/nar/19.19.5275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Wenzel R., Herrmann R. Repetitive DNA sequences in Mycoplasma pneumoniae. Nucleic Acids Res. 1988 Sep 12;16(17):8337–8350. doi: 10.1093/nar/16.17.8337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Yang Y., Ames G. F. DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8850–8854. doi: 10.1073/pnas.85.23.8850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Zakian V. A. Structure and function of telomeres. Annu Rev Genet. 1989;23:579–604. doi: 10.1146/annurev.ge.23.120189.003051. [DOI] [PubMed] [Google Scholar]
  69. Zuerner R. L., Bolin C. A. Repetitive sequence element cloned from Leptospira interrogans serovar hardjo type hardjo-bovis provides a sensitive diagnostic probe for bovine leptospirosis. J Clin Microbiol. 1988 Dec;26(12):2495–2500. doi: 10.1128/jcm.26.12.2495-2500.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. de Bruijn F. J. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol. 1992 Jul;58(7):2180–2187. doi: 10.1128/aem.58.7.2180-2187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]