Publications

GIRAUDO P., SIMONNOT Q., PFLIEGER D., PETER J., GAGLIARDI D. and ZUBER H.

Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing.

In: Eugene Valkov, Aaron C. Goldstrohm (eds) Deadenylation. Methods in Molecular Biology, vol 2723. Humana New York, NY., 2024. | DOI : doi: 10.1007/978-1-0716-3481-3_14

ELSER D., PFLIEGER D., VILLETTE C., MOEGLE B., MIESCH L. and GAQUEREL E.

Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations

Science Advances, 9(34), 2023. | DOI : 10.1126/sciadv.ade8984

KRIEGER C., HALTER D., BALTENWECK R., COGNAT V., BOISSINOT S., MAIA-GRONDARD A., ERDINGER M., BOGAERT F., PICHON E., HUGUENEY P., BRAULT V. and ZIEGLER-GRAFF V.

An aphid-transmitted virus reduces the host plant response to its vector to promote its transmission

Phytopathology, 113(9):1745-1760, 2023. | DOI : 10.1094/PHYTO-12-22-0454-FI

ARRIVÉ M., BRUGGEMAN M., SCALTSOYIANNES V., COUDRAY L., QUAN Y.F.P., SCHELCHER C., COGNAT V., HAMMANN P., CHICHER J., WOLFF P., GOBERT A. and GIEGÉ P.

A tRNA modifying enzyme facilitates RNase P activity in Arabidopsis nuclei.

Nature Plants, 9, 2031-2041, 2023.

ARSÈNE-PLOETZE F., ROMPAIS M., ALIOUA A., COGNAT V., ERHARDT M., GRAINDORGE S., KOECHLER S., MUTTERER J., CARAPITO C. and SCHALLER H.

Streptomyces cocklensis DSM 42063 and Actinacidiphila bryophytorum DSM 42138 colonize Arabidopsis thaliana and modulate its proteome

Phytofrontiers, , 2023. | DOI : doi.org/10.1094/PHYTOFR-12-22-0149-R

GRAINDORGE S., VILLETTE C., KOECHLER S., GROH C., COMTET-MARRE S., MERCIER P., MAGERAND R., PEYRET P., HEINTZ D., SCHALLER H. and ARSÈNE-PLOETZE F.

The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont

International Journal of Molecular Sciences, 23:12952, 2022.

COGNAT V., PAWLAK G., PFLIEGER D. and MARÉCHAL-DROUARD L.

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

Plant Journal, 0, 2022. | DOI : 10.1111/tpj.15997

ELSER D., PFLIEGER D., VILLETTE C., MOEGLE B., MIESCH L. and GAQUEREL E.

Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights allopolyploidy-mediated innovations in N-acylnornicotine metabolism

Science Advances, , 2022.

SCHEER H., DE ALMEIDA C., FERRIER E., SIMONNOT Q., POIRIER L., PFLIEGER D., SEMENT F., KOECHLER S., PIERMARIA C., KRAWCZYK P., MROCZEK S., CHICHER J., KUHN L., DZIEMBOWSKI A., HAMMANN P., ZUBER H. and GAGLIARDI D.

The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Nature Communications, 12:1298, 2021. | DOI : 10.1038/s41467-021-21382-2

FERTET A., GRAINDORGE S., KOECHLER S., DE BOER G.J., GUILLOTEAU-FONTENY E. and GUALBERTO J.M.

Sequence of the mitochondrial genome of Lactuca virosa suggests an unexpected role in Lactuca sativa’s evolution

Frontiers in Plant Science, 12:697136, 2021. | DOI : doi: 10.3389/fpls.2021.697136

CLAVEL M., LECHNER E., INCARBONE M., VINCENT T., COGNAT V., SMIRNOVA E., LECORBEILLER M., BRAULT V., ZIEGLER-GRAFF V. and GENSCHIK P.

Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV

Nucleic Acid Research, 11274–11293, 2021. | DOI : 10.1093/nar/gkab802

MARQUIS V., SMIRNOVA E., GRAINDORGE S., DELCROS P., VILLETTE C., ZUMSTEG J., HEINTZ D. and HEITZ T.

Broad-spectrum stress tolerance conferred by suppressing jasmonate signaling attenuation in Arabidopsis JASMONIC ACID OXIDASE (JAO) mutants

Plant Journal, in press, 2021. | DOI : 10.1111/TPJ.15598

BÖHRER M., RYMEN B., HIMBER C., GERBAUD A., PFLIEGER D., LAUDENCIA-CHINGCUANCO D., CARTWRIGHT A., VOGEL J., SIBOUT R. and BLEVINS T.

Integrated genome-scale analysis and northern blot detection of retrotransposon siRNAs across plant species

In: Heinlein M. (ed) RNA tagging. Methods in Molecular Biology, vol 2166. Humana New York, NY., 2020. | DOI : 10.1007/978-1-0716-0712-1_23

GOSWAMI R., ASNACIOS A., MILANI P., GRAINDORGE S., HOULNÉ G., MUTTERER J., HAMANT O. and CHABOUTÉ M.E.

Mechanical shielding in plant nuclei.

Current Biology, 2013-2025, 2020. | DOI : 10.1016/j.cub.2020.03.059

GENTRIC N., MASOUD K., JOURNOT R.P., COGNAT V., CHABOUTÉ M.E., NOIR S. and GENSCHIK P.

The F-box-like protein FBL17 is a regulator of DNA-damage response and co-localizes with RETINOBLASTOMA RELATED 1 at DNA lesion sites

Plant Physiology, 20.00188, 2020. | DOI : https://doi.org/10.1104/pp.20.00188

PITZALIS N., AMARI K., GRAINDORGE S., PFLIEGER D., DONAIRE L., WASSENEGGER M., LLAVE C. and HEINLEIN M.

Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

Communications Biology, 3:702, 2020. | DOI : 10.1038/s42003-020-01425-y

HUMMEL G., BERR A., GRAINDORGE S., COGNAT V., UBRIG E., PFLIEGER D., MOLINIER J. and MARÉCHAL-DROUARD L.

Epigenetic silencing of clustered tDNAs in Arabidopsis

Nucleic Acids Research, 48:10297-10312, 2020. | DOI : 10.1093/nar/gkaa766

MONTGOMERY S., TANIZAWA Y., GALIK B., WANG N., ITO T., MOCHIZUKI T., AKIMCHEVA S., BOWMAN J., COGNAT V., MARÉCHAL-DROUARD L., EKKER H., HOUNG S., KOHCHI T., LIN S., LIU L., NAKAMURA Y., VALEEVA L., SHAKIROV E., SHIPPEN D., WEI W., YAGURA M., YAMAOKA S., YAMATO K., LIU C. and BERGER F.

Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochroatin

Current Biology, 30:573-588 e7, 2020. | DOI : 10.1016/j.cub.2019.12.015

GOSWAMI R., ASNACIOS A., MILANI P., GRAINDORGE S., HOULNÉ G., MUTTERER J. and HAMANT O.

Mechanical Shielding in Plant Nuclei.

Current Biology, 8(30):2013-2025, 2020. | DOI : doi: 10.1016/j.cub.2020.03.059

THOMPSON D., COGNAT V., GOODFELLOW M., KOECHLER S., HEINTZ D., CARAPITO C., VAN DORSSELAER A., MAHMOUD H., SANGAL V. and ISMAIL W.

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8.

Frontiers in Microbiology, 968-974, 2020.

MEGEL C., HUMMEL G., LALANDE S., UBRIG E., COGNAT V., MORELLE G., SALINAS-GIEGÉ T., DUCHÊNE A.M. and MARÉCHAL-DROUARD L.

Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis

Nucleic Acids Research, 47(2):941-952, 2019. | DOI : 10.1093/nar/gky1156

LANGE H., NDECKY S., GOMEZ-DIAZ C., PFLIEGER D., BUTEL N., ZUMSTEG J., KUHN L., PIERMARIA C., CHICHER J., CHRISTIE M., KARAASLAN E.S., LANG P.L., WEIGEL D., VAUCHERET H., HAMMANN P. and GAGLIARDI D.

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

Nature Communications, 10:3871, 2019. | DOI : 10.1038/s41467-019-11807-4

GRAINDORGE S., COGNAT V., JOHANN TO BERENS P., MUTTERER J. and MOLINIER J.

Photodamage repair pathways contribute to the accurate maintenance of the DNA methylome landscape upon UV exposure

PLoS Genetics, 15(11):e1008476, 2019. | DOI : 10.1371/journal.pgen.1008476

LE RET M., BELCHER S., GRAINDORGE S., WALLET C., KOECHLER S., ERHARDT M., WILLIAMS-CARRIER R., BARKAN A. and GUALBERTO J.M.

An organellar thymidine kinase is required for the efficient replication of the maize plastidial genome.

Plant Physiology, 178:1643-1656, 2018. | DOI : 10.1104/pp.18.00976

MONTAVON T., KWON Y., ZIMMERMANN A., HAMMANN P., VINCENT T., COGNAT V., BERGDOLL M., MICHEL F. and DUNOYER P.

Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates.

Plant Journal, 95(2):204-218, 2018. | DOI : doi: 10.1111/tpj.13941

SCHALK C., COGNAT V., GRAINDORGE S., VINCENT T., VOINNET O. and MOLINIER J.

Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE BINDING protein 2 and ARGONAUTE 1

Proceedings of the National Academy of Sciences of the United States of America, , 2017. | DOI : 10.1073/pnas.1618834114

MONTAVON T., KWON Y., ZIMMERMANN A., HAMMANN P., VINCENT T., COGNAT V., MICHEL F. and DUNOYER P.

A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing

Nucleic Acids Research, 45(3):1330-1344, 2017. | DOI : 10.1093/nar/gkw1264

SALINAS-GIEGÉ T., CAVAIUOLO M., COGNAT V., UBRIG E., REMACLE C., DUCHÊNE A.M., VALLON O. and MARÉCHAL-DROUARD L.

Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii

Nucleic Acids Research, 45(22):12963-12973, 2017. | DOI : 10.1093/nar/gkx903

VINCENT T., VINGADASSALON A., UBRIG E., AZEREDO K., SROUR O., COGNAT V., GRAINDORGE S., SALINAS-GIEGÉ T., MARÉCHAL-DROUARD L. and DUCHÊNE A.M.

A genome-scale analysis of mRNAs targeting to plant mitochondria: upstream AUGs in 5’-UTRs reduce mitochondrial association

Plant Journal, 92(6):1132-1142, 2017. | DOI : 10.1111/tpj.13749

CÓRDOBA-CAÑERO D., COGNAT V., ARIZA R., ROLDÁN ARJONA T. and MOLINIER J.

Dual control of ROS1-mediated active DNA demethylation by the DNA DAMAGE BINDING protein 2 (DDB2)

Plant Journal, , 2017. | DOI : 10.1111/tpj.13753

COGNAT V., MORELLE G., MEGEL C., LALANDE S., MOLINIER J., VINCENT T., SMALL I., DUCHÊNE A.M. and MARÉCHAL-DROUARD L.

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is hygly dynamic

Nucleic Acids Research, 45:3460-3472, 2016. | DOI : 10.1093/nar/gkw1122

SCHALK C., DREVENSEK S., KRAMDI A., KASSAM M., AHMED I., COGNAT V., GRAINDORGE S., BERGDOLL M., BAUMBERGER N., HEINTZ D., BOWLER C., GENSCHIK P., BARNECHE F., COLOT V. and MOLINIER J.

DNA DAMAGE BINDING PROTEIN 2 (DDB2) Shapes the DNA Methylation Landscape

Plant Cell, 28:2043-2059, 2016. | DOI : 10.1105/tpc.16.00474

MICHELY S., TOULZA E., SUBIRANA L., UWE J., COGNAT V., MARÉCHAL-DROUARD L., GRIMSLEY N., MOREUA H. and PIGANEAU G.

Evolution of Codon Usage In The Smallest Photosynthetic Eukaryotes And Their Giant Viruses

Genome Biology and Evolution, 5(5):848-859, 2013. | DOI : 10.1093/gbe/evt053

COGNAT V., PAWLAK G., DUCHÊNE A.M., DAUJAT M., GIGANT A., SALINAS-GIEGÉ T., MICHAUD M., GUTMANN B., GIEGÉ P., GOBERT A. and MARÉCHAL-DROUARD L.

PlantRNA, a database for tRNAs of photosynthetic eukaryotes.

Nucleic Acids Research, 41:273-279, 2013. | DOI : 10.1093/nar/gks935

CHEN C.J., SERVANT N., TOEDLING J., SARAZIN A., MARCHAIS A., DUVERNOIS-BERTHET E., COGNAT V., COLOT V., VOINNET O., HEARD E., CIAUDO C. and BARILLOT E.

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

Bioinformatics, 28(23):3147-3149, 2012. | DOI : 10.1093/bioinformatics/bts587

DE LUIS A., MARKMANN K., COGNAT V., HOLT D.B., CHARPENTIER M., PARNISKE M., STOUGAARD J. and VOINNET O.

Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus.

Plant Physiology, 160:2137-2154, 2012. | DOI : 10.1104/pp.112.204883

DUMBLIAUSKAS E., LECHNER E., JACIUBEK M., BERR A., PAZHOUHANDEH M., ALIOUA A., COGNAT V., BRUKHIN V., KONCZ C., GROSSNIKLAUS U., MOLINIER J. and GENSCHIK P.

The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEDEA parental imprinting

EMBO Journal, 30:731-743, 2011. | DOI : 10.1038/emboj.2010.359

MICHAUD M., COGNAT V., DUCHÊNE A.M. and MARÉCHAL-DROUARD L.

A global picture of tRNA genes in plant genomes

Plant Journal, 66:80-93, 2011. | DOI : 10.1111/j.1365-313X.2011.04490.x

VINOGRADOVA E., SALINAS-GIEGÉ T., COGNAT V., REMACLE C. and MARÉCHAL-DROUARD L.

Steady-state levels of imported tRNAs in Chlamydomona mitochondria are correlated with both cytosolic and mitochondrial codon usages

Nucleic Acids Research, 31:1521-1528, 2009.

LANGE H., HOLEC S., COGNAT V., PIEUCHOT L., LE RET M., CANADAY J. and GAGLIARDI D.

Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana.

Molecular and Cellular Biology, 3038-44, 2008. | DOI : 10.1128/MCB.02064-07

COGNAT V., DERAGON J., VINOGRADOVA E., SALINAS-GIEGÉ T., REMACLE C. and MARÉCHAL-DROUARD L.

On the evolution and expression of Chlamydomonas reinhardtii nucleus-encoded transfer RNA genes

Genetics, 179:113-123, 2008.

GIEGÉ P., SWEETLOVE L., COGNAT V. and LEAVER C.

Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis.

Plant Cell, 17, 1497-1512., 2005.