• Nuclear Speckle RNA binding proteins remodel alternative splicing and the non-coding Arabidopsis transcriptome to regulate a cross-talk between auxin and immune responses.Bazin J., Romero N., Rigo R., Charon C., Blein T., Ariel F. and Crespi M.; (2018) Front Plant Sci. 9:1209. doi: 10.3389/fpls.2018.01209.
  • Splicing regulation by long noncoding RNAs.Romero-Barrios N, Legascue MF, Benhamed M, Ariel F, Crespi M. (2018) Nucleic Acids Res. 46(5):2169-2184, doi: 10.1093/nar/gky095.
  • Thermopriming Triggers Splicing Memory in Arabidopsis.Ling Y, Serrano N, Gao G, Atia M, Mokhtar M, Woo YH, Bazin J, Veluchamy A, Benhamed M, Crespi M, Gehring C, Reddy ASN, Mahfouz MM. (2018) J Exp Bot. 69(10):2659-2675. doi: 10.1093/jxb/ery062.
  • Arabidopsis Heat Shock Transcription FactorA1b regulates multiple developmental genes under benign and stress conditions.Albihlal W., Irabonosi O., Blein T., Persad P., Chernukhin I., CrespiM., Bechtold U. and Mullineaux P.,(2018) J. Exp Bot. 69(11):2847-2862. doi: 10.1093/jxb/ery142.



  • Global analysis of ribosome-associated non-coding RNAs unveils new modes of translational regulation. Bazin J, BaerenfallerK, GosaiS, GregoryB, CrespiM and Bailey-Serres J. PNAS (2017),114(46):E10018-E10027. doi: 10.1073/pnas.1708433114.
  • Antisense movement on the clock.Bazin J, Crespi M. (2017) New Phytol. 2017, 216(3):626-628. doi: 10.1111/nph.14769.
  • The microRNA390/TAS3 pathway controls symbiotic nodulation and lateral root growth in Medicago truncatula. Hobecker KV, M Reynoso, P Bustos Sanmamed, J Wen, KS Mysore, M Crespi, F Blanco, ME Zanetti. (2017) Plant Physiology 174(4):2469-2486. doi: 10.1104/pp.17.00464.
  • The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Jégu T; Veluchamy A; Ramirez-Prado JS; Rizzi-Paillet C; Lhomme A; Latrasse D; Vicaire S; Legras S; Jost B; Rougée M; Barneche F; Bergounioux C; Crespi M; Hirt H; Raynaud C; Benhamed M. (2018) Genome Biology  18(1):114. doi: 10.1186/s13059-017-1246-7.
  • The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Hélène Badouin, Jérôme Gouzy, Christopher J. Grassa1, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L. Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill,Nolan C. Kane, John E. Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet,Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu,Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J. Knapp, Zhao Lai,Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R. Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savitri Nambeesan, Thuy Nguyen,Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M. Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H. Rieseberg & Nicolas B. Langlade. (2017) Nature 546(7656):148-152, doi:10.1038/nature22380.
  • Alternative splicing: The lord of the rings. Federico Ariel and Martin Crespi; News and views (2017) Nature Plants, 3, 17065, DOI: 10.1038/nplants.2017.65.
  • TMV induces RNA decay pathways to modulate gene silencing and disease symptoms. Conti, G.; Zavallo, D.; Venturuzzi, A.; Rodriguez, M.; Crespi, M.; Asurmendi, S. (2017) Plant J. 89(1):73-84. doi: 10.1111/tpj.13323.



  • One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants. Ranjan Swarup, Martin Crespi and Malcolm J. Bennett,(2016) Developmental Cell Preview 39(4):383-385, doi: 10.1016/j.devcel.2016.11.002.
  • Small RNA profiles from soybean primary root tips in response to water deficit identifies a critical role for miRNAs in adaptation to stress. Zheng Y, Hivrale V, Valliyodan B, Lelandais-Brière C,Farmer AD,. May GD, Crespi M, Nguyen HT and Sunkar R. (2016). BMC Systems Biology, 10(Suppl 5):126. doi: 10.1186/s12918-016-0374-0.
  • LHP1 regulates H3K27me3 spreading and shapes the three-dimensional conformation of the Arabidopsis genome. Veluchamy A, Jégu T, Ariel F, Latrasse D, Mariappan K.G, Kim S.K,. Bendahmane A, Crespi M, Hirt H, Bergounioux C, Raynaud C and Benhamed M. (2016). PLOS One, 11(7):e0158936. doi: 10.1371/journal.pone.
  • Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway.Hanemian M, Barlet X, Sorin C, Yadeta K.A, Keller H, Favery B, Simon R, Thomma P.H.J, Hartmann C, Crespi M, Marco Y, Tremousaygue D and L. Deslandes. (2016). New Phytol., 211(2):502-15. doi: 10.1111/nph.
  • The nuclear ribonucleoprotein SmD1 interplays with splicing, RNA quality control and post-transcriptional gene silencing in Arabidopsis. Elvira-Matelot E, Bardou F, Ariel F, Jauvion V, Bouteiller N, Le Masson I, Cao J, Crespi M and Vaucheret H. (2016). The Plant Cell, 28(2), 426-38. doi: 10.1105/tpc.15.01045.
  • Put your 3D glasses on: plant chromatin is on show. N. Y. Rodriguez-Granados, J. S. Ramirez-Prado, A. Veluchamy, D. Latrasse, C. Raynaud, M. Crespi, F. Ariel and M. Benhamed. J. Exp Bot. (2016) 67(11):3205-21. doi: 10.1093/jxb/erw168.
  • Non coding RNAs, emerging regulators in root endosymbioses. C. Lelandais-Brière, J. Moreau, C. Hartmann and M. Crespi, Molec. Plant Microbe Interactions MPMI, 29(3):170-80. doi: 10.1094/MPMI-10-15-0240-FI.
  • Detection of Generic Differential RNA Processing Events from RNA-seq Data. Van Du T., Souiai O., Romero-Barrios N., Crespi M. and Gautheret D. (2016) RNA Biology, 13(1):59-67. doi: 10.1080/15476286.2015.1118604.
  • The chloroplastic DEVH-box helicase ISE2 involved in plasmodesmata regulation is required for group II intron splicing. Carlotto N, Wirth S, Furman N, Ferreyra Solari N, Ariel F, Crespi M, Kobayashi K.Plant Cell Environ. (2016) 39(1):165-73 doi: 10.1111/pce.12603.



  • Battles and hijacks: noncoding transcription in plants. Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M.Trends Plant Sci. 2015 Jun;20(6):362-71. doi: 10.1016/j.tplants.2015.03.003
  • In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs. Martínez de Alba AE, Moreno AB, Gabriel M, Mallory AC, Christ A, Bounon R, Balzergue S, Aubourg S, Gautheret D, Crespi MD, Vaucheret H, Maizel A. (2015) Nucleic Acids Res. 2015 Mar 11;43(5):2902-13. doi: 10.1093/nar/gkv119.



  • Non coding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.
    F. Ariel, T. Jegu, D. Latrasse, N. Romero-Barrios, A. Christ, M. Benhamed and M Crespi (2014) Molecular Cell 55(3):383-96. doi: 10.1016/j.molcel.2014.06.011
  • Long non-coding RNA modulate alternative splicing regulators in Arabidopsis.
    Bardou F, Ariel F, Simpson C, Romero-Barrios N, Laporte P, Balzergue S, Brown J and Crespi M (2014) Developmental Cell 30(2):166-76. doi: 10.1016/j.devcel.2014.06.017
  • The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.
    Formey D, Sallet E, Lelandais-Brière C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier J, Debellé F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J, Crespi M. (2014) Genome Biol. 15(9):457. doi: 10.1186/s13059-014-0457-4
  • A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development.
    Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC, Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C. Plant Biotechnol J. 2014 Jul 24. doi: 10.1111/pbi.12230.
  • Abiotic stress responses in legumes: Strategies used to cope with environmental challenges
    Araújo S. S., Beebe S., Crespi M., Delbreil B., González E. M., Gruber V., Lejeune-Henaut I., Link W., Monteros M. J., Prats E., Rao I., Vadez V., and Vaz Patto M. C. Critical reviews in plant sciences (Legume issue), 2014. doi: 10.1080/07352689.2014.898450
  • A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis
    C. Sorin, M. Declerck, A. Christ, T. Blein, L. Ma,  C. Lelandais-Brière, M. F. Njo, T. Beeckman, M. Crespi and C. Hartmann. New Phytol. (2014)202(4):1197-1211. doi: 10.1111/nph.12735
  • The SWI/SNF chromatin remodelling protein AtBAF60 directly controls the formation of a gene loop at the FLC locus in Arabidopsis
    T. Jégu, D. Latrasse, M. Delarue, H. Hirt, S. Domenichini, F. Ariel, M. Crespi, C. Bergounioux, C. Raynaud and M. Benhamed (2014) Plant Cell 26(2):538-51. doi: 10.1105/tpc.113.114454





  • Multiple functions of KRP5 connect endoreduplication and cell elongation.
    Jegu T., Latrasse D., Delarue M., Mazubert C., Bourge M., Hudik E., Blanchet S., Soler M.N., Charon C., Crespi M., De Veylder L., Raynaud C., Bergounioux C., and Benhamed M. (2013) Plant Physiology, 161, 1694. doi: 10.1104/pp.112.212357
  • Localization in nuclear compartments of a bacterial group II intron-encoded protein in eukaryotic cells is consistent with the evolution of these retroelements to spliceosomal introns
    R. Nisa-Martínez, P. Laporte, J. I. Jiménez-Zurdo, F. Frugier, M. Crespi and N. Toro. (2013) PLoS One 8(12):e84056. doi: 10.1371/journal.pone.0084056
  • miR160 overexpression affects root growth and nitrogen-fixing nodule number in Medicago truncatula
    P. Bustos-Sanmamed, G. Mao, Y. Deng, M. Elouet, G. A. Khan, J. Bazin, M. Turner, S. Subramanian, O. Yu, M. Crespi and C. Lelandais-Brière (2013) Functional Plant Biology. 40(12):1208-1220.doi: 10.1071/FP13123.
  • Small RNA pathways and diversity in model legumes: lessons from genomics
    P. Bustos-Sanmamed, J. Bazin, C. Hartmann, M. Crespi, C. Lelandais-Brière (2013) Front Plant Sci. 4:236.doi: 10.3389/fpls.2013.00236.
  • Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti.
    O. Torres-Quesada, V. Millán, R. Nisa-Martínez, F. Bardou, M. Crespi, N. Toro and J. I. Jiménez-Zurdo 2013, PLOS One 8(7):e68147. doi: 10.1371/journal.pone.0068147.
  • miR396 affects mycorrhization and root meristem activity in the legume Medicago truncatula
    J. Bazin, G. Khan, J.P. Combier, P. Bustos-Sanmamed, J. M. Debernardi, R. Rodriguez, C. Sorin, J. Palatnik, C. Hartmann, M. Crespi and C. Lelandais-Briere 2013, Plant J. 74(6):920-34. doi: 10.1111/tpj.12178
  • Cytoplasmic and nuclear quality control and turnover of single stranded RNA modulate post-transcriptional gene silencing in plants.
    A. Moreno, A. Martínez de Alba, F. Bardou, M. Crespi, H., Vaucheret, A. Maizel, A. Mallory (2013) Nucleic Acids Res., 41(8), 4699-4708. doi: 10.1093/nar/gkt152.
  • Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator.
    D. Latrasse, T. Jégu1, Pin-Hong Meng, C. Mazubert, E. Hudik, M. Delarue, C. Charon, M. Crespi, H. Hirt, C. Raynaud, C. Bergounioux and M. Benhamed, 2013, Nucleic Acids Research, (2013), 41(5), 2907-17. doi: 10.1093/nar/gks1458.
  • In silico identification and in vivo validation of a set of evolutionary conserved plant root-specific cis-regulatory elements
    A. Christ, I. Maegele, N. Ha, H. Ha Nguyen, M. Crespi and A. Maizel, Mechanisms of development, (2013) 130(1):70-81. doi: 10.1016/j.mod.2012.03.002






  • Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection in Medicago truncatula
    M. Reynoso, F. Blanco, J. Bailey-Serres, M. Crespi and M. E. Zanetti (2012) Plant J. 2012 doi: 10.1111/tpj.12033.
  • Two direct targets of cytokinin signaling control symbiotic nodulation
    F. Ariel, M. Brault-Hernandez, C. Laffont, E. Huault, M. Brault, J. Plet, M. Moison, S. Blanchet, J. L. Ichanté, M. Chabaud, S. Carrere, M. Crespi, R. L. Chan and F. Frugier. Plant Cell, 2012, 24(9):3838-52. doi: 10.1105/tpc.112.103267
  • Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis
    V. Jouannet, A. B. Moreno, T. Elmayan, H. Vaucheret, M. Crespi and A. Maizel, EMBO J., 2012, 31(7):1704-13. doi: 10.1038/emboj.2012.20
  • Comparative transcriptomic analysis of salt adaptation in roots of contrasting Medicago truncatula genotypes
    O. Zahaf, S. Blanchet, A. de Zelicourt, B. Alunni, J. Plet, C. Laffont, L. de Lorenzo, S. Imbeaud, J-L. Ichanté, A. Diet, M. Badri, A. Zabalza, E. M. González, H. Delacroix, V. Gruber, F. Frugier and M. Crespi. Molecular Plant 2012; 5(5):1068-81. doi: 10.1093/mp/sss009
  • Complexity of miRNA-dependent regulation in root symbiosis
    J. Bazin, P. Bustos-Sanmameda, C. Hartmann, C. Lelandais-Brièrea and M. Crespi. Philos. Transactions of the Royal Society, 367(1595):1570-9. doi: 10.1098/rstb.2011.0228
  • Dual implication of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence
    A. de Zelicourt, A. Diet, J. Marion, C. Laffont, F. Ariel, M. Moison, Z. Ons, M. Crespi, V. Gruber and F. Frugier. Plant J. (2012), 70(2):220-30. doi: 10.1111/j.1365-313X.2011.04859.x






  • Dual RNAs in plants
    F. Bardou, F. Merchan, F. Ariel and M. Crespi Biochimie (2011) 11:1950-4. doi: 10.1016/j.biochi.2011.07.028
  • MicroRNAs as regulators of root development and architecture
    G. Khan, M. Declerck, C. Sorin, C. Hartmann, M. Crespi and C. Lelandais-Brière. Plant Mol. Biol. (2011) 77: 47-58. doi: 10.1007/s11103-011-9793-x
  • Transcriptional and posttranscriptional regulation of a NAC1 transcription factor in Medicago truncatula roots
    K. D’Haeseleer, G. Den Herder, C. Laffont, J. Plet, V. Mortier, C. Lelandais-Brière, S. De Bodt, A. De Keyser, M. Crespi, M. Holsters, F. Frugier and S. Goormachtig New Phytol (2011)191:647-61. doi: 10.1111/j.1469-8137.2011.03719.x
  • A novel fry1 allele reveals the existence of a mutant phenotype unrelated to 5’->3’ exoribonuclease (XRN) activities in Arabidopsis thaliana roots
    J. Hirsch, J. Misson, P. A. Crisp, P. David, V. Bayle, G. M. Estavillo, H. Javot, S. Chiarenza, A. C. Mallory, A. Maizel, M. Declerck, B. J. Pogson, H. Vaucheret, M. Crespi, T. Desnos, M.C. Thibaud, L. Nussaume and E. Marin PLOS one (2011),6(2):e16724. doi: 10.1371/journal.pone.0016724
  • MtCRE1-dependent cytokinin signaling integrates bacterial and plant cues to coordinate symbiotic nodule organogenesis in Medicago truncatula
    J. Plet, A. Wasson, F. Ariel, C. Le Signor, D. Baker, U. Mathesius, M. Crespi and F. Frugier Plant J. (2011) 65, 622-633. doi: 10.1111/j.1365-313X.2010.04447.x
  • Regulation of nonsymbiotic and truncated leghemoglobin genes of Lotus japonicus in plants organs and in response to nitric oxide and hormones
    Bustos-Sanmamed P., Tovar-Mendeza A., Crespi M., Sato S., Tabata S. and Becana M. New Phytol. (2011) 189(3):765-76. doi: 10.1111/j.1469-8137.2010.03527.x






  • Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor Mt HB1.
    F. Ariel, A. Diet, M. Verdenaud, V. Gruber, F. Frugier, R. Chan and M. Crespi. Plant Cell (2010) 22(7): 2171-83. doi: 10.1105/tpc.110.074823
  • The LOB-like transcription factor MtLBD1 controls Medicago truncatula root architecture under salt stress
    F. D. Ariel, A. Diet, M. Crespi and R. Chan(2010) Plant Signaling and Behaviour, 5:12, 1-3 doi: 10.4161/psb.5.12.14020
  • Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus
    C. Charon, A. B. Moreno, F. Bardou and M. Crespi. Mol Plant (2010) 3: 729-739. doi: 10.1093/mp/ssq037
  • The Compact Root Architecture 1 gene regulates lignification, flavonoid production and polar auxin transport in Medicago truncatula
    C. Laffont, S. Blanchet, C. Lapierre, L. Brocard, P. Ratet, M. Crespi, U. Mathesius and F. Frugier. Plant Physiol. (2010) 153(4):1597-607. doi: 10.1104/pp.110.156620
  • miR390, TAS3 ta-siRNAs andtheir ARF targets define an auto-regulatory network quantitatively controlling lateral root growth.
    V. Jouannet, E. Marin, A. Herz, A.S. Lokerse, D. Weijers, H. Vaucheret, L. Nussaume, M. D. Crespi and A. Maizel. Plant Cell (2010) 22(4):1104-1 doi: 10.1105/tpc.109.072553
  • A novel RNA-binding peptide regulates the establishment of the Medicago truncatula - Sinorhizobium meliloti nitrogen-fixing symbiosis
    P. Laporte, B. Satiat-Jeunemaitre, I. Velasco, T. Csorba, W. Van de Velde, A. Campalans, J. Burgyan, M. Arevalo-Rodriguez and M. Crespi. Plant J. (2010) 62 (1): 24-38. doi: 10.1111/j.1365-313X.2009.04121.x
  • Cleavage of a non-conserved target by a specific miR156 isoform in root apexes of Medicago truncatula
    L. Naya, G. Khan, C. Sorin, C. Hartmann, M. Crespi and C. Lelandais-Brière. Plant Signaling and Behaviour (2010) 5(3):1-4. doi: 10.4161/psb.5.3.11190
  • Small RNA diversity in plants and its impact in development
    C. Lelandais-Brière, C. Sorin, M. Declerck, A. Benslimane, M. Crespi and C. Hartmann, Current Genomics (2010) 11(1), 14-23. doi: 10.2174/138920210790217918.



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