Publications

2023

Liehrmann A, Delannoy E, Launay-Avon A, Gilbault E, Loudet O, Castandet B, Rigaill G. DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection. NAR Genom Bioinform. 2023 Nov 6;5(4):lqad098. https://doi.org/10.1093/nargab/lqad098

Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Sultan K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science. 2023 Sep;381(6661):eadg0995. https://doi.org/10.1126/science.adg0995

Delannoy E, Batardiere B, Pateyron S, Soubigou-Taconnat L, Chiquet J, Colcombet J, Lang J. Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq. Plant Commun. 2023 Aug 28:100676. https://doi.org/10.1016/j.xplc.2023.100676

Castandet, B., Lurin, C., Delannoy, É., Monachello, D. (2023). High-Throughput Protein–Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline. In: Mukhtar, S. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 2690. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3327-4_16

2022

Baudry K, Delannoy E, Colas des Francs-Small C. Analysis of the Plant Mitochondrial Transcriptome. Methods Mol Biol. 2022;2363:235-262. https://doi.org/10.1007/978-1-0716-1653-6_17. 

Baudry K, Barbut F, Domenichini S, Guillaumot D, Thy MP, Vanacker H, Majeran W, Krieger-Liszkay A, Issakidis-Bourguet E, Lurin C. Adenylates regulate Arabidopsis plastidial thioredoxin activities through the binding of a CBS domain protein. Plant Physiol. 2022 Aug 1;189(4):2298-2314. https://doi.org/10.1093/plphys/kiac199. 

Baudry K, Paysant-Le Roux C, Colella S, Castandet B, Martin-Magniette ML. (2022)  Analyzing multifactorial RNA-Seq experiments with DicoExpress JoVE, https://doi.org/10.3791/62566

2021

Monachello D, Lauraine M, Gillot S, Michel F, Costa M. A new RNA-DNA interaction required for integration of group II intron retrotransposons into DNA targets. Nucleic Acids Res. 2021 Dec 2;49(21):12394-12410. https://doi.org/10.1093/nar/gkab1031. 

Marine Guilcher, Arnaud Liehrmann, Chloé Seyman, Thomas Blein, Guillem Rigaill, Benoit Castandet, Etienne Delannoy. (2021) Full length transcriptome highlights the coordination of plastid transcript processing. International journal of Molecular Sciences. https://doi.org/10.3390/ijms222011297.

Jakalski Marcin, Minasiewicz Julita, Caius José, May Michal, Selosse Marc-André, Delannoy Etienne. The Genomic Impact of Mycoheterotrophy in Orchids. Front Plant Sci. 2021 Jun 9; 12:1084.  https://doi.org/10.3389/fpls.2021.632033 
 
2020    

Current status of the multinational Arabidopsis community. Parry G, Provart NJ, Brady SM, Uzilday B; Multinational Arabidopsis Steering Committee. Plant Direct. 2020 Aug 2;4(7):e00248. https://doi.org/10.1002/pld3.248. 

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis. MacIntosh GC, Castandet B. Plant Physiol. 2020 Aug;183(4):1438-1452. https://doi.org/10.1104/pp.20.00076

Livia Merendino, Florence Courtois, Björn Grübler, Olivier Bastien, Vera Straetmanns, Fabien Chevalier, Silva Lerbs-Mache, Claire Lurin, Thomas Pfannschmidt. 2020. Philosophical Transactions of the Royal Society B, (2020) https://doi.org/10.1098/rstb.2019.0567

Manuel González-Fuente, Sébastien Carrère, Dario Monachello, Benjamin G. Marsella, Anne-Claire Cazalé, Claudine Zischek,NathalieRezé,Ludovic Cottret, Shahid M. Mukhtar, Claire Lurin, Laurent D. Noël and Nemo Peeters 2020 . Mol Plant Pathol. 21(10):1257-1270 EffectorK, a comprehensive resource to mine for pathogen effector targets in the Arabidopsis proteome. https://doi.org/10.1101/2019.12.16.878074

Fabien Chardon, Gwendal Cueff, Etienne Delannoy, Fabien Aubé, Aurélia Lornac, Magali Bedu, Françoise Gilard, Stéphanie Pateyron, Hélène Rogniaux, Audrey Gargaros, Hakim Mireau, Loïc Rajjou, Marie-Laure Martin-Magniette, Françoise Budar (2020) The consequences of a disruption in cyto-nuclear co adaptation on the molecular response to a nitrate starvation in Arabidopsis. Plants https://doi.org/10.3390/plants9050573
 
Malbert B, Burger M, Lopez-Obando M, Baudry K, Launay-Avon A, Härtel B, Verbitskiy D, Jörg A, Berthomé R, Lurin C, Takenaka M, Delannoy E. (2020) The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins. Plants https://doi.org/10.3390/plants9020280
 
2019    

Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res. 2019 Dec 16;47(22):11889-11905 https://doi.org/10.1101/621938

Lallemand F, Logacheva M, Le Clainche I, Bérard A, Zheleznaia E, May M, Jakalski M, Delannoy E, Le Paslier MC, Selosse MA. Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids. Genome Biol Evol. 2019 Sep 1;11(9):2457-2467. https://doi.org/10.1093/gbe/evz170

Adnan Khan Niazi, Etienne Delannoy, Rana Khalid Iqbal, Daria Mileshina, Romain Val, Marta Gabryelska, Eliza Wyszko, Ludivine Soubigou-Taconnat, Maciej Szymanski, Jan Barciszewski, Frédérique Weber-Lotfi, José Manuel Gualberto, André Dietrich (2019) Mitochondrial transcriptome control and inter-compartment cross-talk during plant development. Cells https://doi.org/10.3390/cells8060583
 
Lallemand F, Martin-Magniette ML, Gilard F, Gakière B, Launay-Avon A, Delannoy É, Selosse MA. (2019) In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi. Plant Journal https://doi.org/10.1111/tpj.14276
 
2018    

Majeran W, Le Caer JP, Ponnala L, Meinnel T, Giglione C. (2018). Targeted Profiling of Arabidopsis thaliana Subproteomes Illuminates Co- and Posttranslationally N-Terminal Myristoylated Proteins. Plant Cell. 30(3):543-562.  https://doi.org/10.1105/tpc.17.00523
 
Michel EJS, Hotto AM, Strickler SR, Stern DB, Castandet B. (2018) A Guide to the Chloroplast Transcriptome Analysis Using RNA-Seq. Methods Mol Biol. 1829:295-313.  https://doi.org/10.1007/978-1-4939-8654-5_20
 
Courtois F, Merendino L. (2018) Mapping Plastid Transcript Population by Circular Reverse Transcription Polymerase Chain Reaction. Methods Mol Biol. 1829:273-278.  https://doi.org/10.1007/978-1-4939-8654-5_18

Malbert B, Rigaill G, Brunaud V, Lurin C, Delannoy E. Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing. Methods Mol Biol. 2018;1829:279-294. doi:10.1007/978-1-4939-8654-5_19. https://doi.org/10.1007/978-1-4939-8654-5_19

2017    
 
Guillaumot D, Lopez-Obando M, Baudry K, Avon A, Rigaill G, Falcon de Longevialle A, Broche B, Takenaka M, Berthomé R, De Jaeger G, Delannoy E, Lurin C. (2017) Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. PNAS https://doi.org/10.1073/pnas.1705780114
 
Balzergue C, Dartevelle T, Godon C, Laugier E, Meisrimler C, Teulon JM, Creff A, Bissler M, Brouchoud C, Hagège A, Müller J, Chiarenza S, Javot H, Becuwe-Linka N, David P, Péret B, Delannoy E, Thibaud MC, Armengaud J, Abel S, Pellequer JL, Nussaume L, Desnos T. Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation. Nat Commun. 2017 May 15;8:15300. https://doi.org/10.1038/ncomms15300
 
Citerne HL, Reyes E, Le Guilloux M, Delannoy E, Simonnet F, Sauquet H, Weston PH, Nadot S, Damerval C. Characterization of CYCLOIDEA-like genes in Proteaceae, a basal eudicot family with multiple shifts in floral symmetry. Ann Bot. 2017 Feb;119(3):367-378. https://doi.org/10.1093/aob/mcw219