BIBLIOGRAPHY


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Reviews on repeats

Gilson E., Saurin W., Perrin D., Bachellier S. and Hofnung M. (1991) The BIME family of bacterial highly repetitive sequences. Res. Microbiol. 142: 217-222.


Bachellier S., Gilson E., Hofnung M. and Hill C.W. (1996) Repeated sequences. In : Escherichia coli and Salmonella Cellular and Molecular Biology. Neidhardt F.C. et al. editors. ASM Press, Washington D.C. pp 2012-2040.


Bachellier S., Clément J.M. and Hofnung M. (1999) Short palindromic repetitive DNA elements in enterobacteria : a survey. Res. Microbiol. 150: 627-639.

General articles

Kunisawa T. and Nakamura M. (1991) Identification of regulatory building blocks in Escherichia coli genome. Protein Seq. Data Anal. 4: 43-47.


Leung M-Y., Blaisdell B.E., Burge C. and Karlin S. (1991) An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J. Mol. Biol. 221: 1367-1378.


Blaisdell B.E., Rudd K.E., Matin A. and Karlin A. (1993) Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups. J. Mol. Biol. 229: 833-848.


BIMEs

Higgins C.F., Ferro-Luzzi Ames G., Barnes W.M., Clément J-M. and Hofnung M. (1982) A novel intercistronic regulatory element of prokaryotic operons. Nature 298 :760-762.


Gilson E., Clément J-M., Brutlag D. and Hofnung M. (1984) A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3: 1417-1421.


Stern M.J., Ferro-Luzzi Ames G., Smith N.H., Robinson E.C. and Higgins C.J. (1984) Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37: 1015-10126.


Gilson E., Rousset J-P., Clément J-M. and Hofnung M. (1986) A subfamily of E. coli Palindromic Units implicated in transcription termination? Ann. Inst. Pasteur/ Microbiol. 137 B :259-270.


Gilson E., Perrin D., Clément J-M., Szmelcman S., Dassa E. and Hofnung M. (1986) Palindromic Units from E. coli as binding sites for a chromoid-associated protein. FEBS Lett. 206: 323-328.


Gilson E., Perrin D., Saurin W. and Hofnung M. (1987) Species specificity of bacterial Palindromic Units. J. Mol. Evol. 25 :371-373.


Newbury S.F., Smith N.H. and Higgins C.F. (1987) Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51: 1131-1143.


Newbury S.F., Smith N.H., Robinson E.C., Hiles I.D. and Higgins C.F. (1987) Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48: 297-310.


Stern M.J., Prossnitz E. and Ferro-Luzzi Ames G. (1988) 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. 2: 141-152.


Yang Y. and Ferro-Luzzi Ames G. (1988) DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc. Natl. Acad. Sci. USA 85: 8850-8854.


Gilson E., Perrin D. and Hofnung M. (1990) DNA polymerase I and a protein complex bind specifically to E. coli Palindromic Unit highly repetitive DNA : implications for bacterial chromosome organization. Nucl. Acids Res. 18: 3941-3952.


Gilson E., Saurin W., Perrin D., Bachellier S. and Hofnung M. (1991) Palindromic Units are part of a new Bacterial Interspersed Mosaic Element (BIME). Nucl. Acids Res. 19: 1375-1383.


Bachellier S., Perrin D., Hofnung M. and Gilson E. (1993) Bacterial Interspersed Mosaic Elements (BIMEs) are present in the genome of Klebsiella. Mol. Microbiol. 7: 537-544.


Boccard F. and Prentki P. (1993) Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3' end of transcription units. EMBO J. 12: 5019-5027.


Oppenheim A.B., Rudd K.E., Mendelson I. and Teff D. (1993) Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli. Mol Microbiol. 10: 113-122.


Bachellier S., Saurin W., Perrin D., Hofnung M. and Gilson E. (1994) Structural and functional diversity among Bacterial Interspersed Mosaic Elements (BIMEs). Mol. Microbiol.12: 61-70.


Engelhorn M., Boccard F., Murtin C., Prentki P. and Geiselmann J. (1995) In vivo interaction of the Escherichia coli integration host factor with its specific binding sites. Nucl. Acids Res. 23: 2959-2965.


Bachellier S., Clément J.M., Hofnung M. and Gilson E. (1997) Bacterial Interspersed Mosaic Elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145: 551-562.


Espéli O. and Boccard F. (1997) In vivo cleavage of Escherichia coli BIME-2 repeat by DNA gyrase : genetic characterization of the target and identification of the cut site. Mol. Microbiol. 26: 767-777.


Clément J.M., Wilde C., Bachellier S., Lambert P. and Hofnung M. (1999) IS1397 is active for transposition into the chromosome of Escherichia coli K-12 and inserts specifically into Palindromic Units of Bacterial Interspersed Mosaic Elements. J. Bacteriol. 181: 6929-6936.


BOCEs

Bergler H., Högenauer G. and Turnowski F. (1992) Sequences of the envM gene and two mutated alleles in Escherichia coli. J. Gen. Microbiol. 138: 2093-2100.


Bachellier S., Clément J.M. and Hofnung M. (1999) Short palindromic repetitive DNA elements in enterobacteria : a survey. Res. Microbiol. 150: 627-639.


29 bp repeats

Nakata A., Amemura M. and Makino K. (1989) Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171: 3553-3556.


Mojica F.J.M., Diez-Villaseñor C., Soria E. and Juez G. (2000) Biological significance of a family of regularly spaced repeats in the genomes of Archea, Bacteria and mitochondria. Mol. Microbiol. 36: 244-246.


IRUs/ERICs

Sharples G.J. and Lloyd R.G. (1990) A novel repeated DNA sequence located in the intergenic regions of bacterial chromosome. Nucl. Acids Res. 18: 6503-6508.


Hulton C.S.J., Higgins C.F. and Sharp, P.M. (1991) ERIC sequences : a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5: 825-834.


Versalovic J., Koeuth T., Britton R., Geszvain K. and Lupski J.R. (1993) Conservation and evolution of the rpsU-dnaG-rpoD macromolecular synthesis operon in bacteria. Mol. Microbiol. 8: 343-355.


Cromie G., Collins J. and Leach D. (1997) Sequence interruptions in enterobacterial repeated elements retain their ability to encode well-folded RNA secondary structures. Mol. Microbiol. 24: 1311-1314.


Sharp P.M. (1997) Insertions within ERIC sequences. Mol. Microbiol. 24: 1314-1315.


RSAs

Mizobuchi K. (1993) Systematic sequencing of the Escherichia coli genome. Personal Communication. First International Symposium mapping and Sequencing of Small Genomes, Institut Pasteur, Paris.


Bouché J.P. (1995) BEE95: a novel sequence family related to IRU/ERIC dispersed enterobacterial intergenic elements. Mol. Microbiol. 18: 987-989.


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Please send questions and comments to Sophie.Bachellier@pasteur.fr.