Publications
2007
Mandin P., Repoila F., Vergassola M., Geissmann T., Cossart P.
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets Article de journal
Dans: Nucleic Acids Res, vol. 35, no. 3, p. 962-74, 2007, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | BibTeX | Étiquettes: 5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism
@article{,
title = {Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets},
author = { P. Mandin and F. Repoila and M. Vergassola and T. Geissmann and P. Cossart},
year = {2007},
date = {2007-01-01},
journal = {Nucleic Acids Res},
volume = {35},
number = {3},
pages = {962-74},
abstract = {To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA-mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism},
pubstate = {published},
tppubtype = {article}
}
2002
Cristofari G., Bampi C., Wilhelm M., Wilhelm F. X., Darlix J. L.
A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition Article de journal
Dans: EMBO J, vol. 21, no. 16, p. 4368-79, 2002, (0261-4189 Journal Article).
Résumé | BibTeX | Étiquettes: *Gene, *Transcription, Acid, cerevisiae/*genetics, Complementary/biosynthesis, Conformation, DNA, Expression, Fungal, Fungal/chemistry/*metabolism, Genetic, Gov't, in, Messenger/chemistry/*metabolism, Non-U.S., Nucleic, Phylogeny, Regulation, Retroelements/*genetics, RNA, Saccharomyces, Support, vitro
@article{,
title = {A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition},
author = { G. Cristofari and C. Bampi and M. Wilhelm and F. X. Wilhelm and J. L. Darlix},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {16},
pages = {4368-79},
abstract = {LTR-retrotransposons are abundant components of all eukaryotic genomes and appear to be key players in their evolution. They share with retroviruses a reverse transcription step during their replication cycle. To better understand the replication of retrotransposons as well as their similarities to and differences from retroviruses, we set up an in vitro model system to examine minus-strand cDNA synthesis of the yeast Ty1 LTR-retrotransposon. Results show that the 5' and 3' ends of Ty1 genomic RNA interact through 14 nucleotide 5'-3' complementary sequences (CYC sequences). This 5'-3' base pairing results in an efficient initiation of reverse transcription in vitro. Transposition of a marked Ty1 element and Ty1 cDNA synthesis in yeast rely on the ability of the CYC sequences to base pair. This 5'-3' interaction is also supported by phylogenic analysis of all full-length Ty1 and Ty2 elements present in the Saccharomyces cerevisiae genome. These novel findings lead us to propose that circularization of the Ty1 genomic RNA controls initiation of reverse transcription and may limit reverse transcription of defective retroelements.},
note = {0261-4189
Journal Article},
keywords = {*Gene, *Transcription, Acid, cerevisiae/*genetics, Complementary/biosynthesis, Conformation, DNA, Expression, Fungal, Fungal/chemistry/*metabolism, Genetic, Gov't, in, Messenger/chemistry/*metabolism, Non-U.S., Nucleic, Phylogeny, Regulation, Retroelements/*genetics, RNA, Saccharomyces, Support, vitro},
pubstate = {published},
tppubtype = {article}
}