Mandin P., Repoila F., Vergassola M., Geissmann T., Cossart P.
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets Journal Article
In: Nucleic Acids Res, vol. 35, no. 3, pp. 962-74, 2007, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | BibTeX | Tags: 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}
}
Grosjean H., Keith G., Droogmans L.
Detection and quantification of modified nucleotides in RNA using thin-layer chromatography Book Section
In: Gott, J. M. (Ed.): RNA Interference, Editing, and Modification: Methods and Protocols, vol. 265, pp. 357-91, Springer Protocols, Humana Press, 2004.
Abstract | BibTeX | Tags: &, 5', acids, and, Base, Chromatography, Composition, Deoxyribonucleotides/chemistry/isolation, DNA/chemistry/genetics/isolation, Endoribonucleases, Gov't, Indicators, Isotope, KEITH, Labeling/methods, Layer/methods, Non-U.S., Nucleic, Oligoribonucleotides/chemistry/isolation, Peptide, purification, Radioisotopes, Reagents, Regions/chemistry, Ribonucleotides/*analysis, RNA/*genetics/isolation, Support, Thin, Untranslated
@incollection{,
title = {Detection and quantification of modified nucleotides in RNA using thin-layer chromatography},
author = { H. Grosjean and G. Keith and L. Droogmans},
editor = { J.M. Gott},
year = {2004},
date = {2004-01-01},
booktitle = {RNA Interference, Editing, and Modification: Methods and Protocols},
volume = {265},
pages = {357-91},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.},
keywords = {&, 5', acids, and, Base, Chromatography, Composition, Deoxyribonucleotides/chemistry/isolation, DNA/chemistry/genetics/isolation, Endoribonucleases, Gov't, Indicators, Isotope, KEITH, Labeling/methods, Layer/methods, Non-U.S., Nucleic, Oligoribonucleotides/chemistry/isolation, Peptide, purification, Radioisotopes, Reagents, Regions/chemistry, Ribonucleotides/*analysis, RNA/*genetics/isolation, Support, Thin, Untranslated},
pubstate = {published},
tppubtype = {incollection}
}