Publications
2021
Alghoul F, Eriani G, Martin F
RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT Chapitre d'ouvrage
Dans: Rederstorff, M (Ed.): Methods Mol Biol, vol. 2300, p. 241-250, Springer Protocols, Humana Press, New York, NY, 2021, ISBN: 978-1-0716-1385-6/ISSN, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN
@inbook{Alghoul2021,
title = {RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT},
author = {F Alghoul and G Eriani and F Martin},
editor = {M Rederstorff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792883},
doi = {10.1007/978-1-0716-1386-3_18},
isbn = {978-1-0716-1385-6/ISSN},
year = {2021},
date = {2021-01-01},
booktitle = {Methods Mol Biol},
volume = {2300},
pages = {241-250},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
series = {Methods in Molecular Biology},
abstract = {RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
2020
Ali L M, Pitchai F N, Vivet-Boudou V, Chameettachal A, Jabeen A, Pillai V N, Mustafa F, Marquet R, Rizvi T A
Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation Article de journal
Dans: Frontiers in Microbiology, no. 11, p. 595410, 2020.
Résumé | Liens | BibTeX | Étiquettes: base paired purines, MARQUET, Mason-Pfizer monkey virus, PAILLART, retroviruses, RNA packaging, RNA secondary structure, RNA-Gag interaction, SHAPE, single-stranded purines, Unité ARN
@article{L.2020,
title = {Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation },
author = {L M Ali and F N Pitchai and V Vivet-Boudou and A Chameettachal and A Jabeen and V N Pillai and F Mustafa and R Marquet and T A Rizvi
},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.595410/full},
doi = { 10.3389/fmicb.2020.595410 },
year = {2020},
date = {2020-11-05},
journal = {Frontiers in Microbiology},
number = {11},
pages = {595410},
abstract = {A distinguishing feature of the Mason-Pfizer monkey virus (MPMV) packaging signal RNA secondary structure is a single-stranded purine-rich sequence (ssPurines) in close vicinity to a palindromic stem loop (Pal SL) that functions as MPMV dimerization initiation site (DIS). However, unlike other retroviruses, MPMV contains a partially base-paired repeat sequence of ssPurines (bpPurines) in the adjacent region. Both purine-rich sequences have earlier been proposed to act as potentially redundant Gag binding sites to initiate the process of MPMV genomic RNA (gRNA) packaging. The objective of this study was to investigate the biological significance of ssPurines and bpPurines in MPMV gRNA packaging by systematic mutational and biochemical probing analyses. Deletion of either ssPurines or bpPurines individually had no significant effect on MPMV gRNA packaging, but it was severely compromised when both sequences were deleted simultaneously. Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) analysis of the mutant RNAs revealed only mild effects on structure by deletion of either ssPurines or bpPurines, while the structure was dramatically affected by the two simultaneous deletions. This suggests that ssPurines and bpPurines play a redundant role in MPMV gRNA packaging, probably as Gag binding sites to facilitate gRNA capture and encapsidation. Interestingly, the deletion of bpPurines revealed an additional severe defect on RNA propagation that was independent of the presence or absence of ssPurines or the gRNA structure of the region. These findings further suggest that the bpPurines play an additional role in the early steps of MPMV replication cycle that is yet to be identified. },
keywords = {base paired purines, MARQUET, Mason-Pfizer monkey virus, PAILLART, retroviruses, RNA packaging, RNA secondary structure, RNA-Gag interaction, SHAPE, single-stranded purines, Unité ARN},
pubstate = {published},
tppubtype = {article}
}