Publications

2022

Rodriguez-Granados NY, Ramirez-Prado JS, Brik-Chaouche R, An J, Manza-Mianza D, Sircar S, Troadec C, Hanique M, Soulard C, Costa R, Dogimont C, Latrasse D, Raynaud C, Boualem A, Benhamed M, Bendahmane A (2022) CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo). Plant J 109: 1213–1228

Pichot C, Djari A, Tran J, Verdenaud M, Marande W, Huneau C, Gautier V, Latrasse D, Arribat S, Sommard V, Troadec C, Poncet C, Bendahmane M, Szecsi J, Dogimont C, Salse J, Benhamed M, Zouine M, Boualem A, Bendahmane A (2022) Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 25: 103696

Roulé T, Christ A, Hussain N, Huang Y, Hartmann C, Benhamed M, Gutierrez-Marcos J, Ariel F, Crespi M, Blein T (2022) The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA. Mol Plant 15: 840–856

Zhao F, Tian S, Wu Q, Li Z, Ye L, Zhuang Y, Wang M, Xie Y, Zou S, Teng W, Tong Y, Tang D, Mahato, AK, Benhamed M, Liu Z, Zhang Y (2022) Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae. Plant Commun 3: 100304

Fonouni-Farde C, Christ A, Blein T, Legascue MF, Ferrero L, Moison M, Lucero L, Ramírez-Prado JS, Latrasse D, Gonzalez D, Benhamed, M, Quadrana L, Crespi M, Ariel F (2022) The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants. Genome Biol 23: 181

Nomoto Y, Takatsuka H, Yamada K, Suzuki TT, Suzuki TT, Huang Y, Latrasse D, An J, Gombos M, Breuer C, Ishida T, Maeo K, Imamura M, Yamashino T, Sugimoto K, Magyar Z, Bögre L, Raynaud C, Benhamed M, Ito M (2022) A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis. Nat Commun 13: 1660

Chevigny N, Weber-Lotfi F, Le Blevenec A, Nadiras C, Fertet A, Bichara M, Erhardt M, Dietrich A, Raynaud C, Gualberto JM (2022) RADA-dependent branch migration has a predominant role in plant mitochondria and its defect leads to mtDNA instability and cell cycle arrest. PLoS Genet 18: e1010202

2021

Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M (2021) Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. New Phytol 229: 902–919

Juery C, Concia L, De Oliveira R, Papon N, Ramírez-González R, Benhamed M, Uauy C, Choulet F, Paux E (2021) New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome 14: e20069

Moison M, Pacheco JM, Lucero L, Fonouni-Farde C, Rodríguez-Melo J, Mansilla N, Christ A, Bazin J, Benhamed M, Ibañez F, Crespi M, Estevez JM, Ariel F (2021) The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. Mol Plant 14: 937–948

Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM (2021) Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 4: 529

Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M Ntoukakis V (2021) Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog 17: e1009572

Ramirez-Prado JS, Benhamed M (2021) New partners for old friends: Plant SWI/SNF complexes. Mol Plant 14: 870–872

Jacob P, Brisou G, Dalmais M, Thévenin J, van der Wal F, Latrasse D, Suresh Devani R, Benhamed M, Dubreucq B, Boualem A, Lepiniec L, Immink RGH, Hirt H, Bendahmane A (2021) The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis. Genes (Basel). doi: 10.3390/genes12050746

Ramirez-Prado JS, Latrasse D, Benhamed M (2021) Histone Modification ChIP-seq on Arabidopsis thaliana Plantlets. Bio-protocol 11: e4211

Nisa M, Bergis C, Pedroza-Garcia J-A, Drouin-Wahbi J, Mazubert C, Bergounioux C, Benhamed M, Raynaud C (2021) The plant DNA polymerase theta is essential for the repair of replication-associated DNA damage. Plant J 106: 1197–1207

Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S, Probst AV, Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M (2021) Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. Genome Res. doi: 10.1101/gr.273771.120

Zhang J, Augustine RC, Suzuki M, Feng J, Char SN, Yang B, McCarty DR, Vierstra RD (2021) The SUMO ligase MMS21 profoundly influences maize development through its impact on genome activity and stability. PLOS Genet 17: e1009830

Pedroza-Garcia JA, Eekhout T, Achon I, Nisa M-U, Coussens G, Vercauteren I, Van den Daele H, Pauwels L, Van Lijsebettens M, Raynaud C, De Veylder L (2021) Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death. Plant Cell 33: 2662–2684

2020

Huang Y, Rodriguez-Granados NY, Latrasse D, Raynaud C, Benhamed M, Ramirez-Prado JS (2020) The matrix revolutions: towards the decoding of the plant chromatin three-dimensional reality. J Exp Bot 71: 5129–5147

Roldan MVG, Izhaq F, Verdenaud M, Eleblu J, Haraghi A, Sommard V, Chambrier P, Latrasse D, Jégu T, Benhamed M, Szécsi J, Bendahmane M, Boualem A, Bendahmane A (2020) Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development. Commun Biol 3: 239

Lakhssassi N, Piya S, Bekal S, Liu S, Zhou Z, Bergounioux C, Miao L, Meksem J, Lakhssassi A, Jones K, Kassem M A, Benhamed M, Bendahmane A, Lambert K, Boualem A, Hewezi T, Meksem K (2020) A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines. Plant Biotechnol J 18: 1810–1829

Rigo R, Bazin J, Romero-Barrios N, Moison M, Lucero L, Christ A, Benhamed M, Blein T, Huguet S, Charon C, Crespi M, Ariel F (2020) The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors. EMBO Rep 21: e48977

Bruggeman Q, Piron-Prunier F, Tellier F, Faure J-D, Latrasse D, Manza-Mianza D, Mazubert C, Citerne S, Boutet-Mercey S, Lugan R, Bergounioux C, Raynaud C, Benhamed M, Delarue M (2020) Involvement of Arabidopsis BIG protein in cell death mediated by Myo-inositol homeostasis. Sci Rep 10: 11268

Nájera-Martínez M, Pedroza-García JA, Suzuri-Hernández LJ, Mazubert C, Drouin-Wahbi J, Vázquez-Ramos J, Raynaud C, Plasencia J (2020) Maize Thymidine Kinase Activity Is Present throughout Plant Development and Its Heterologous Expression Confers Tolerance to an Organellar DNA-Damaging Agent. Plants (Basel, Switzerland) 9: 930

Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D, Benhamed M (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 21: 104

Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J (2020) A new role for histone demethylases in the maintenance of plant genome integrity. Elife. doi: 10.7554/eLife.58533

Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M (2020) GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5’ and 3’ ends of its target genes. Nucleic Acids Res 48: 5953–5966

Bourguet P, López-González L, Gómez-Zambrano Á, Pélissier T, Hesketh A, Potok ME, Pouch-Pélissier M-N, Perez M, Da Ines O, Latrasse D, White CI, Jacobsen SE, Benhamed M, Mathieu O (2020) DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. Genome Biol 21: 283

Ariel F, Lucero L, Christ A, Mammarella MF, Jegu T, Veluchamy A, Mariappan K, Latrasse D, Blein T, Liu C, Benhamed M, Crespi M (2020) R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Mol Cell 77: 1055-1065.e4

2019

Völz R, Kim S-K, Mi J, Rawat AA, Veluchamy A, Mariappan KG, Rayapuram N, Daviere J-M, Achard P, Blilou I, Benhamed M, Crespi M (2019) INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana. PLoS Pathog 15: e1007499

Pedroza-Garcia J-A, De Veylder L, Raynaud C (2019) Plant DNA polymerases. Int J Mol Sci. doi: 10.3390/ijms20194814

Chumová J, Kourová H, Trögelová L, Halada P, Binarová P (2019) Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed? Cells. doi: 10.3390/cells8030259

Nisa M-U, Huang Y, Benhamed M, Raynaud C (2019) The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions. Front Plant Sci 10

Pedroza-García J-A, Nájera-Martínez M, Mazubert C, Aguilera-Alvarado P, Drouin-Wahbi J, Sánchez-Nieto S, Gualberto JM, Raynaud C, Plasencia J (2019) Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity. Plant J 97: 430–446

Camborde L, Raynaud C, Dumas B, Gaulin E (2019) DNA-Damaging Effectors: New Players in the Effector Arena. Trends Plant Sci 24: 1094–1101

Tissot N, Robe K, Gao F, Grant-Grant S, Boucherez J, Bellegarde F, Maghiaoui A, Marcelin R, Izquierdo E, Benhamed M, Martin A, Vignols F, Roschzttardtz H, Gaymard F, Briat JF, Dubos C (2019) Transcriptional integration of the responses to iron availability in Arabidopsis by the bHLH factor ILR3. New Phytol 223: 1433–1446

Fiorucci A-S, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas A-F, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F (2019) Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 20: 100

Ramirez-Prado JS, Latrasse D, Rodriguez-Granados NY, Huang Y, Manza-Mianza D, Brik-Chaouche R, Jaouannet M, Citerne S, Bendahmane A, Hirt H, et al (2019) The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity. Plant J 100: 1118–1131

Betsch L, Boltz V, Brioudes F, Pontier G, Girard VV, Savarin J, Wipperman B, Chambrier P, Tissot N, Benhamed M, Mollereau B, Raynaud C, Bendahmane M, Szécsi J (2019) TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals. PLoS Genet 15: e1007899

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