Brunel C, Ehresmann C
Secondary structure of the 3' UTR of bicoid mRNA Journal Article
In: Biochimie, vol. 86, no. 2, pp. 91-104, 2004, ISBN: 15016447, (0300-9084 Journal Article).
Abstract | Links | BibTeX | Tags: Biological *Nucleic Acid Conformation RNA, BRUNEL 3' Untranslated Regions/*chemistry/genetics Animals Conserved Sequence Dimerization Drosophila Homeodomain Proteins/*genetics Models, Messenger/biosynthesis/*chemistry/genetics RNA-Binding Proteins/chemistry/genetics Regulatory Sequences, Non-U.S. Gov't Trans-Activators/*genetics, Nucleic Acid/genetics Support, Unité ARN
@article{,
title = {Secondary structure of the 3' UTR of bicoid mRNA},
author = {C Brunel and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15016447},
isbn = {15016447},
year = {2004},
date = {2004-01-01},
journal = {Biochimie},
volume = {86},
number = {2},
pages = {91-104},
abstract = {Formation of the Bicoid morphogen gradient in early Drosophila embryos requires the pre-localization of bicoid mRNA to the anterior pole of the egg. The program of bcd mRNA localization involves multiples steps and proceeds from oogenesis until early embryogenesis. This process requires cis-elements in the 3' UTR of bcd mRNA and successive and/or concomitant critical protein interactions. Furthermore, numerous RNA elements and binding proteins contribute to regulate bcd expression. In the present paper, we investigated the secondary structure of the full length 3' UTR of the bcd mRNA, using a variety of chemical and enzymatic structural probes. This RNA probing analysis allowed us to give a detailed description of the 3' UTR of the bcd mRNA and its organization into five well-defined and independent domains (I-V). One prominent result that emerges from our data is the unexpected high degree of flexibility of the different domains relative to each others. This plasticity relies upon the open conformation of the central hinge region interconnecting domains II, III, and IV + V. Otherwise, dimerization of the 3' UTR, which participates to anchoring bcd mRNA at the anterior pole of the embryo, only results in discrete and local change in domain III. Domain I that contains sites for trans-acting factors exhibiting single stranded RNA binding specificity is mainly unstructured. By contrast, each core domains (II-V) is highly organized and folds into helices interrupted by bulges and interior loops and closed by very exposed apical loops. These elements mostly built specific determinants for trans-acting factors. Besides, these findings provide a valuable database for structure/function studies.},
note = {0300-9084
Journal Article},
keywords = {Biological *Nucleic Acid Conformation RNA, BRUNEL 3' Untranslated Regions/*chemistry/genetics Animals Conserved Sequence Dimerization Drosophila Homeodomain Proteins/*genetics Models, Messenger/biosynthesis/*chemistry/genetics RNA-Binding Proteins/chemistry/genetics Regulatory Sequences, Non-U.S. Gov't Trans-Activators/*genetics, Nucleic Acid/genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wagner C, Palacios I, Jaeger L, Johnston D St, Ehresmann B, Ehresmann C, Brunel C
Dimerization of the 3'UTR of bicoid mRNA involves a two-step mechanism Journal Article
In: J Mol Biol, vol. 313, no. 3, pp. 511-524, 2001, ISBN: 11676536, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 3' Untranslated Regions/*chemistry/genetics/*metabolism Animals Base Pairing Base Sequence Biological Transport Dimerization Drosophila Proteins/genetics/metabolism Drosophila melanogaster/embryology/*genetics/metabolism Genes, Biological Mutation/genetics *Nucleic Acid Conformation Oligonucleotides/chemistry/genetics/metabolism Protein Transport RNA-Binding Proteins/metabolism Regulatory Sequences, Insect/genetics Homeodomain Proteins/*genetics Kinetics Models, Non-U.S. Gov't Thermodynamics Trans-Activators/*genetics, Nucleic Acid/genetics Support, Unité ARN
@article{,
title = {Dimerization of the 3'UTR of bicoid mRNA involves a two-step mechanism},
author = {C Wagner and I Palacios and L Jaeger and D St Johnston and B Ehresmann and C Ehresmann and C Brunel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11676536},
isbn = {11676536},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {313},
number = {3},
pages = {511-524},
abstract = {The proper localization of bicoid (bcd) mRNA requires cis-acting signals within its 3' untranslated region (UTR) and trans-acting factors such as Staufen. Dimerization of bcd mRNA through intermolecular base-pairing between two complementary loops of domain III of the 3'UTR was proposed to be important for particle formation in the embryo. The participation in the dimerization process of each domain building the 3'UTR was evaluated by thermodynamic and kinetic analysis of various mutated and truncated RNAs. Although sequence complementarity between the two loops of domain III is required for initiating mRNA dimerization, the initial reversible loop-loop complex is converted rapidly into an almost irreversible complex. This conversion involves parts of RNA outside of domain III that promote initial recognition, and dimerization can be inhibited by sense or antisense oligonucleotides only before conversion has proceeded. Injection of the different bcd RNA variants into living Drosophila embryos shows that all elements that inhibit RNA dimerization in vitro prevent formation of localized particles containing Staufen. Particle formation appeared to be dependent on both mRNA dimerization and other element(s) in domains IV and V. Domain III of bcd mRNA could be substituted by heterologous dimerization motifs of different geometry. The resulting dimers were converted into stable forms, independently of the dimerization module used. Moreover, these chimeric RNAs were competent in forming localized particles and recruiting Staufen. The finding that the dimerization domain of bcd mRNA is interchangeable suggests that dimerization by itself, and not the precise geometry of the intermolecular interactions, is essential for the localization process. This suggests that the stabilizing interactions that are formed during the second step of the dimerization process might represent crucial elements for Staufen recognition and localization.},
note = {0022-2836
Journal Article},
keywords = {3' Untranslated Regions/*chemistry/genetics/*metabolism Animals Base Pairing Base Sequence Biological Transport Dimerization Drosophila Proteins/genetics/metabolism Drosophila melanogaster/embryology/*genetics/metabolism Genes, Biological Mutation/genetics *Nucleic Acid Conformation Oligonucleotides/chemistry/genetics/metabolism Protein Transport RNA-Binding Proteins/metabolism Regulatory Sequences, Insect/genetics Homeodomain Proteins/*genetics Kinetics Models, Non-U.S. Gov't Thermodynamics Trans-Activators/*genetics, Nucleic Acid/genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Helm M, Brule H, Friede D, Giege R, Putz D, Florentz C
Search for characteristic structural features of mammalian mitochondrial tRNAs Journal Article
In: RNA, vol. 6, no. 10, pp. 1356-1379, 2000, ISBN: 11073213, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Animals Base Pairing Base Sequence *Computational Biology Escherichia coli/genetics Genome Human Molecular Sequence Data Multigene Family *Nucleic Acid Conformation RNA/*chemistry/genetics RNA Stability RNA, Amino Acid-Specific/*chemistry/genetics Regulatory Sequences, FLORENTZ, Non-U.S. Gov't Variation (Genetics), Nucleic Acid/genetics Support, Transfer, Unité ARN
@article{,
title = {Search for characteristic structural features of mammalian mitochondrial tRNAs},
author = {M Helm and H Brule and D Friede and R Giege and D Putz and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073213},
isbn = {11073213},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1356-1379},
abstract = {A number of mitochondrial (mt) tRNAs have strong structural deviations from the classical tRNA cloverleaf secondary structure and from the conventional L-shaped tertiary structure. As a consequence, there is a general trend to consider all mitochondrial tRNAs as "bizarre" tRNAs. Here, a large sequence comparison of the 22 tRNA genes within 31 fully sequenced mammalian mt genomes has been performed to define the structural characteristics of this specific group of tRNAs. Vertical alignments define the degree of conservation/variability of primary sequences and secondary structures and search for potential tertiary interactions within each of the 22 families. Further horizontal alignments ascertain that, with the exception of serine-specific tRNAs, mammalian mt tRNAs do fold into cloverleaf structures with mostly classical features. However, deviations exist and concern large variations in size of the D- and T-loops. The predominant absence of the conserved nucleotides G18G19 and T54T55C56, respectively in these loops, suggests that classical tertiary interactions between both domains do not take place. Classification of the tRNA sequences according to their genomic origin (G-rich or G-poor DNA strand) highlight specific features such as richness/poorness in mismatches or G-T pairs in stems and extremely low G-content or C-content in the D- and T-loops. The resulting 22 "typical" mammalian mitochondrial sequences built up a phylogenetic basis for experimental structural and functional investigations. Moreover, they are expected to help in the evaluation of the possible impacts of those point mutations detected in human mitochondrial tRNA genes and correlated with pathologies.},
note = {1355-8382
Journal Article},
keywords = {Acylation Animals Base Pairing Base Sequence *Computational Biology Escherichia coli/genetics Genome Human Molecular Sequence Data Multigene Family *Nucleic Acid Conformation RNA/*chemistry/genetics RNA Stability RNA, Amino Acid-Specific/*chemistry/genetics Regulatory Sequences, FLORENTZ, Non-U.S. Gov't Variation (Genetics), Nucleic Acid/genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}