Acknowledgements requested in publications
« This work of the Interdisciplinary Thematic Institute IMCBio, as part of the ITI 2021-2028 program of the University of Strasbourg, CNRS and Inserm, was supported by IdEx Unistra (ANR-10-IDEX-0002), and by SFRI-STRAT’US project (ANR 20-SFRI-0012) and EUR IMCBio (ANR-17-EURE-0023) under the framework of the French Investments for the Future Program. »
2018
J., Trachman R.; Abdolahzadeh, A; Andreoni, A; Cojocaru, R; Knutson, J R; Ryckelynck, M; Unrau, P J; Ferre-D'Amare, A R
Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness Article de journal
Dans: Biochemistry, vol. 57, no. 26, p. 3544-3548, 2018, ISBN: 29768001, (1520-4995 (Electronic) 0006-2960 (Linking) Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.).
@article{nokey,
title = {Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness},
author = {Trachman R. J. and A Abdolahzadeh and A Andreoni and R Cojocaru and J R Knutson and M Ryckelynck and P J Unrau and A R Ferre-D'Amare},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=29768001},
doi = {10.1021/acs.biochem.8b00399},
isbn = {29768001},
year = {2018},
date = {2018-01-01},
journal = {Biochemistry},
volume = {57},
number = {26},
pages = {3544-3548},
abstract = {Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with approximately 1 nM affinity and enhances its fluorescence by >1500-fold, was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity. Mutational analysis of the binding site led to Mango-II(A22U), which retains high affinity for TO1-Biotin but now discriminates >5-fold against TO3-biotin. Moreover, fluorescence enhancement of TO1-Biotin increases by 18%, while that of TO3-Biotin decreases by 25%. Crystallographic, spectroscopic, and analogue studies show that the A22U mutation improves conformational homogeneity and shape complementarity of the fluorophore-RNA interface. Our work demonstrates that even after extensive functional selection, aptamer RNAs can be further improved through structure-guided engineering.},
note = {1520-4995 (Electronic)
0006-2960 (Linking)
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Creugny, A; Fender, A; Pfeffer, S
Regulation of primary-microRNA processing Article de journal
Dans: FEBS Lett, vol. 592, no. 12, p. 1980-1996, 2018, ISBN: 29683487.
@article{nokey,
title = {Regulation of primary-microRNA processing},
author = {A Creugny and A Fender and S Pfeffer},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29683487?dopt=Abstract},
doi = {10.1002/1873-3468.13067},
isbn = {29683487},
year = {2018},
date = {2018-01-01},
journal = {FEBS Lett},
volume = {592},
number = {12},
pages = {1980-1996},
abstract = {MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the fine-tuning of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated. This article is protected by copyright. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vaseva, II; Qudeimat, E; Potuschak, T; Du, Y; Genschik, P; Vandenbussche, F; Straeten, D Van Der
The plant hormone ethylene restricts Arabidopsis growth via the epidermis Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 115, no. 17, p. E4130-E4139, 2018, ISBN: 29643073, (1091-6490 (Electronic) 0027-8424 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {The plant hormone ethylene restricts Arabidopsis growth via the epidermis},
author = {II Vaseva and E Qudeimat and T Potuschak and Y Du and P Genschik and F Vandenbussche and D Van Der Straeten},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=29643073},
doi = {10.1073/pnas.1717649115},
isbn = {29643073},
year = {2018},
date = {2018-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {115},
number = {17},
pages = {E4130-E4139},
abstract = {The gaseous hormone ethylene plays a key role in plant growth and development, and it is a major regulator of stress responses. It inhibits vegetative growth by restricting cell elongation, mainly through cross-talk with auxins. However, it remains unknown whether ethylene controls growth throughout all plant tissues or whether its signaling is confined to specific cell types. We employed a targeted expression approach to map the tissue site(s) of ethylene growth regulation. The ubiquitin E3 ligase complex containing Skp1, Cullin1, and the F-box protein EBF1 or EBF2 (SCF(EBF1/2)) target the degradation of EIN3, the master transcription factor in ethylene signaling. We coupled EBF1 and EBF2 to a number of cell type-specific promoters. Using phenotypic assays for ethylene response and mutant complementation, we revealed that the epidermis is the main site of ethylene action controlling plant growth in both roots and shoots. Suppression of ethylene signaling in the epidermis of the constitutive ethylene signaling mutant ctr1-1 was sufficient to rescue the mutant phenotype, pointing to the epidermis as a key cell type required for ethylene-mediated growth inhibition.},
note = {1091-6490 (Electronic)
0027-8424 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zuber, H; Scheer, H; Joly, A C; Gagliardi, D
Respective Contributions of URT1 and HESO1 to the Uridylation of 5' Fragments Produced From RISC-Cleaved mRNAs Article de journal
Dans: Front Plant Sci, vol. 9, p. 1438, 2018, ISBN: 30364210, (1664-462X (Print) 1664-462X (Linking) Journal Article).
@article{nokey,
title = {Respective Contributions of URT1 and HESO1 to the Uridylation of 5' Fragments Produced From RISC-Cleaved mRNAs},
author = {H Zuber and H Scheer and A C Joly and D Gagliardi},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=30364210},
doi = {10.3389/fpls.2018.01438},
isbn = {30364210},
year = {2018},
date = {2018-01-01},
journal = {Front Plant Sci},
volume = {9},
pages = {1438},
abstract = {In plants, post-transcriptional gene silencing (PTGS) represses gene expression by translation inhibition and cleavage of target mRNAs. The slicing activity is provided by argonaute 1 (AGO1), and the cleavage site is determined by sequence complementarity between the target mRNA and the microRNA (miRNA) or short interfering RNA (siRNA) loaded onto AGO1, to form the core of the RNA induced silencing complex (RISC). Following cleavage, the resulting 5' fragment is modified at its 3' end by the untemplated addition of uridines. Uridylation is proposed to facilitate RISC recycling and the degradation of the RISC 5'-cleavage fragment. Here, we detail a 3' RACE-seq method to analyze the 3' ends of 5' fragments produced from RISC-cleaved transcripts. The protocol is based on the ligation of a primer at the 3' end of RNA, followed by cDNA synthesis and the subsequent targeted amplification by PCR to generate amplicon libraries suitable for Illumina sequencing. A detailed data processing pipeline is provided to analyze nibbling and tailing at high resolution. Using this method, we compared the tailing and nibbling patterns of RISC-cleaved MYB33 and SPL13 transcripts between wild-type plants and mutant plants depleted for the terminal uridylyltransferases (TUTases) HESO1 and URT1. Our data reveal the respective contributions of HESO and URT1 in the uridylation of RISC-cleaved MYB33 and SPL13 transcripts, with HESO1 being the major TUTase involved in uridylating these fragments. Because of its depth, the 3' RACE-seq method shows at high resolution that these RISC-generated 5' RNA fragments are nibbled by a few nucleotides close to the cleavage site in the absence of uridylation. 3' RACE-seq is a suitable approach for a reliable comparison of uridylation and nibbling patterns between mutants, a prerequisite to the identification of all factors involved in the clearance of RISC-generated 5' mRNA fragments.},
note = {1664-462X (Print)
1664-462X (Linking)
Journal Article},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vaseva, II; Qudeimat, E; Potuschak, T; Du, Y; Genschik, P; Vandenbussche, F; Straeten, D Van Der
The plant hormone ethylene restricts Arabidopsis growth via the epidermis Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 115, no. 17, p. E4130-E4139, 2018, ISBN: 29643073, (1091-6490 (Electronic) 0027-8424 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {The plant hormone ethylene restricts Arabidopsis growth via the epidermis},
author = {II Vaseva and E Qudeimat and T Potuschak and Y Du and P Genschik and F Vandenbussche and D Van Der Straeten},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=29643073},
doi = {10.1073/pnas.1717649115},
isbn = {29643073},
year = {2018},
date = {2018-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {115},
number = {17},
pages = {E4130-E4139},
abstract = {The gaseous hormone ethylene plays a key role in plant growth and development, and it is a major regulator of stress responses. It inhibits vegetative growth by restricting cell elongation, mainly through cross-talk with auxins. However, it remains unknown whether ethylene controls growth throughout all plant tissues or whether its signaling is confined to specific cell types. We employed a targeted expression approach to map the tissue site(s) of ethylene growth regulation. The ubiquitin E3 ligase complex containing Skp1, Cullin1, and the F-box protein EBF1 or EBF2 (SCF(EBF1/2)) target the degradation of EIN3, the master transcription factor in ethylene signaling. We coupled EBF1 and EBF2 to a number of cell type-specific promoters. Using phenotypic assays for ethylene response and mutant complementation, we revealed that the epidermis is the main site of ethylene action controlling plant growth in both roots and shoots. Suppression of ethylene signaling in the epidermis of the constitutive ethylene signaling mutant ctr1-1 was sufficient to rescue the mutant phenotype, pointing to the epidermis as a key cell type required for ethylene-mediated growth inhibition.},
note = {1091-6490 (Electronic)
0027-8424 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2007
Auffinger, P; Hashem, Y
Nucleic acid solvation: from outside to insight Article de journal
Dans: Curr Opin Struct Biol, vol. 17, no. 3, p. 325-33, 2007, ISBN: 17574833, (0959-440X (Print) 0959-440X (Linking) Journal Article Review).
@article{nokey,
title = {Nucleic acid solvation: from outside to insight},
author = {P Auffinger and Y Hashem},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17574833},
doi = {10.1016/j.sbi.2007.05.008},
isbn = {17574833},
year = {2007},
date = {2007-01-01},
journal = {Curr Opin Struct Biol},
volume = {17},
number = {3},
pages = {325-33},
abstract = {Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations. In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions. Finally, anions can also bind to these polyanionic systems. Many of these recent insights are provided by state-of-the-art molecular dynamics simulations of nucleic acid systems, which will be described together with relevant methodological issues.},
note = {0959-440X (Print)
0959-440X (Linking)
Journal Article
Review},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Auffinger, P; Hashem, Y
SwS: a solvation web service for nucleic acids Article de journal
Dans: Bioinformatics, vol. 23, no. 8, p. 1035-7, 2007, ISBN: 17324939, (1367-4811 (Electronic) 1367-4803 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {SwS: a solvation web service for nucleic acids},
author = {P Auffinger and Y Hashem},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17324939},
doi = {10.1093/bioinformatics/btm067},
isbn = {17324939},
year = {2007},
date = {2007-01-01},
journal = {Bioinformatics},
volume = {23},
number = {8},
pages = {1035-7},
abstract = {UNLABELLED: SwS, based on a statistical analysis of crystallographic structures deposited in the NDB, is designed to provide an exhaustive overview of the solvation of nucleic acid structural elements through the generation of 3D solvent density maps. A first version (v1.0) of this web service focuses on the interaction of DNA, RNA and hybrid base pairs linked by two or three hydrogen bonds with water, cations and/or anions. Data provided by SwS are updated on a weekly basis and can be used by: (i) those involved in molecular dynamics simulation studies for validation purposes; (ii) crystallographers for help in the interpretation of solvent density maps; and all those involved in (iii) drug design and, more generally, in (iv) nucleic acid structural studies. SwS provides also statistical data related to the frequency of occurrence of different types of base pairs in crystallographic structures and the conformation of the involved nucleotides. This web service has been designed to allow a maximum of flexibility in terms of queries and has also been developed with didactic considerations in mind. AVAILABILITY: http://www-ibmc.u-strasbg.fr/arn/sws.html},
note = {1367-4811 (Electronic)
1367-4803 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}