Project 3: Epigenetics and non-coding RNA-mediated regulation

Project 3: Epigenetics and non-coding RNA-mediated regulation

Coordination: Martin Crespi / Hervé Vaucheret


The interplay between small RNAs and other non-coding RNAs, chromatin marks and transcription factors play a decisive role in the control of gene expression. In the last years, small RNAs have been linked to epigenetic changes and post-transcriptional regulation in a variety of differentiation processes and/or diseases in eukaryotes. The capacity of plants to adapt their growth to environmental stimuli through epigenetic modifications that could be transmitted to their progeny strengthens their use for the elucidation of these regulatory mechanisms. The major objective of this project is to understand the action of small and long non-coding RNAs in gene expression and epigenetic regulation and the dynamics of these ncRNA-mediated regulations in plants. We have modified the expression patterns of specific enzymes controlling small RNA production and we characterized potential new epigenetic targets of this mechanism through genome-wide approaches. This has deepened the analysis of the wide utility of this technology to identify new targets in agriculture. We have also identified new links between chromatin regulation and long non-coding RNAs as well as an unexpected connection with alternative splicing regulation. Hence, we provide the basis to address how the non-coding RNA repertoire and/or the RNA-linked machinery can improve the epigenetic potential of plants.


Ariel F., Jegu T., Latrasse D., Romero-Barrios N., Christ A., Benhamed M., Crespi M. (2014). Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop. Molecular Cell 55(3): 383-396.

Ariel F., Romero-Barrios N., Jegu T., Benhamed M., Crespi M. (2015). Battles and hijacks: noncoding transcription in plants. Trends in Plant Science 20(6): 362-371.

Ariel F., Crespi M. (2017). Alternative splicing: The lord of the rings. Nature Plants 3: doi:10.1038/nplants.2017.1065.

Ariel F, Lucero L, Christ A, Mammarella MF, Jegu T, Veluchamy A, Mariappan K, Latrasse D, Blein T, Liu C, Benhamed M and Crespi M (2020) R-loop mediated trans-action of the APOLO long noncoding RNA. Molecular Cell 77(5):1055-1065.e4. doi: 10.1016/j.molcel.2019.12.015.

Bardou F., Ariel F., Simpson C.G., Romero-Barrios N., Laporte P., Balzergue S., Brown J.W.S., Crespi M. (2014). Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis. Developmental Cell 30(2): 166-176.

Bazin J, Baerenfaller K, Gosai S, Gregory B, Crespi M and Bailey-Serres J (2017) Global analysis of ribosome-associated non-coding RNAs unveils new modes of translational regulation. PNAS 114(46):E10018-E10027. doi: 10.1073/pnas.1708433114.

Bazin J, Romero N, Rigo R, Charon C, Blein T, Ariel F and Crespi M (2018) Nuclear Speckle RNA binding proteins remodel alternative splicing and the non-coding Arabidopsis transcriptome to regulate a cross-talk between auxin and immune responses. Frontiers Plant Sci 9:1209. doi: 10.3389/fpls.2018.01209.

Bazin J, Mariappan K, Jiang Y, Blein T, Voelz R, Crespi M and Hirt H (2020) Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. PLOS Pathogens 16(4):e1008401. doi: 10.1371/journal.ppat.1008401.

Blein T, Balzergue C, Roulé T, Gabriel M, Scalisi L, François T, Sorin C, Christ A, Godon C, Delannoy E, Martin-Magniette ML, Nussaume L, Hartmann C, Gautheret D, Desnos T, Crespi M (2020) Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation. Plant Physiol 183(3):1058-1072. doi: 10.1104/pp.20.00446.

Butel, N., Le Masson, I., Bouteiller, N., Vaucheret, H., and Elmayan, T. (2017). sgs1: a neomorphic nac52 allele impairing post-transcriptional gene silencing through SGS3 downregulation. Plant J 90, 505-519.

Butel, N., Yu, A., Le Masson, I., Borges, F., Elmayan, T., Taochy, C., Gursanscky, N.R., Cao, J., Bi, S., Sawyer, A., Carroll, B.J., and Vaucheret, H. (2021). Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis. Nat Commun 12, 2787.

Butt H, Eid A, Momin AA, Bazin J, Crespi M, Arold ST, Mahfouz MM (2019) CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors. Genome Biol 20(1):73. doi: 10.1186/s13059-019-1680-9.

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 Biology (Nature eds) 4(1):529. doi: 10.1038/s42003-021-02051-y.

Cao, J., Gursanscky, N.R., Fletcher, S.J., Sawyer, A., Wadia, M., McKeough, L., Coleman, M., Dressel, U., Taochy, C., Mitter, N., Vaucheret, H., and Carroll, B.J. (2020). Can-Seq: a PCR and DNA sequencing strategy for identifying new alleles of known and candidate genes. Plant Methods 16, 16.

Charbonnel, C., Niazi, A.K., Elvira-Matelot, E., Nowak, E., Zytnicki, M., de Bures, A., Jobet, E., Opsomer, A., Shamandi, N., Nowotny, M., Carapito, C., Reichheld, J.P., Vaucheret, H., and Saez-Vasquez, J. (2017). The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain. Nucleic Acids Res 45, 11891-11907.

Conti G, Zavallo D, Venturuzzi A, Rodriguez M, Crespi M, Asurmendi S (2017) TMV induces RNA decay pathways to modulate gene silencing and disease symptoms. Plant J 89(1):73-84. doi: 10.1111/tpj.13323.

Crespi M (2020) Plant transcription links environmental cues and phenotypic plasticity. Transcription 11(3-4):97-99. doi: 10.1080/21541264.2020. 1837498.

Derrien, B., Clavel, M., Baumberger, N., Iki, T., Sarazin, A., Hacquard, T., Ponce, M.R., Ziegler-Graff, V., Vaucheret, H., Micol, J.L., Voinnet, O., and Genschik, P. (2018). A Suppressor Screen for AGO1 Degradation by the Viral F-Box P0 Protein Uncovers a Role for AGO DUF1785 in sRNA Duplex Unwinding. Plant Cell 30, 1353-1374.

Du, F., Gong, W., Bosca, S., Tucker, M., Vaucheret, H., and Laux, T. (2020). Dose-Dependent AGO1-Mediated Inhibition of the miRNA165/166 Pathway Modulates Stem Cell Maintenance in Arabidopsis Shoot Apical Meristem. Plant Commun 1, 100002.

Elvira-Matelot E., Bardou F., Ariel F., Jauvion V., Bouteiller N., Le Masson I., Cao J., Crespi M.D., Vaucheret H. (2016a). The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis. Plant Cell 28(2): 426-438.

Elvira-Matelot E., Hachet M., Shamandi N., Comella P., Saez-Vasquez J., Zytnicki M., Vaucheret H. (2016b). Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation. Plant Cell 28(2): 406-425.

Fonouni-Farde C, Ariel F, Crespi M (2021) Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations. Noncoding RNA 7(1):12. doi: 10.3390/ncrna7010012

Hematy, K., Bellec, Y., Podicheti, R., Bouteiller, N., Anne, P., Morineau, C., Haslam, R.P., Beaudoin, F., Napier, J.A., Mockaitis, K., Gagliardi, D., Vaucheret, H., Lange, H., and Faure, J.D. (2016). The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis. PLoS Genet 12, e1005817.

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) The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biology 18(1):114. doi: 10.1186/s13059-017-1246-7.

Lange H., Zuber H., Sement F.M., Chicher J., Kuhn L., Hammann P., Brunaud V., Berard C., Bouteiller N., Balzergue S., Aubourg S., Martin-Magniette M.-L., Vaucheret H., Gagliardi D. (2014). The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana. PLOS Genetics 10(8): e1004564.

Lange, H., Ndecky, S.Y.A., Gomez-Diaz, C., Pflieger, D., Butel, N., Zumsteg, J., Kuhn, L., Piermaria, C., Chicher, J., Christie, M., Karaaslan, E.S., Lang, P.L.M., Weigel, D., Vaucheret, H., Hammann, P., and Gagliardi, D. (2019). RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nat Commun 10, 3871.

Lelandais-Brière C, Moreau J, Hartmann C and Crespi M (2016) Non-coding RNAs, emerging regulators in root endosymbiosis. Molec Plant Microbe Interactions MPMI 29(3):170-80. doi: 10.1094/MPMI-10-15-0240-FI.

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) Thermopriming Triggers Splicing Memory in Arabidopsis. J Exp Bot 69(10):2659-2675. doi: 10.1093/jxb/ery062.

Lucero L, Bazin J, Rodriguez Melo J, Ibañez F, Crespi M*, Ariel F* (*co-corresponding authors) (2020) Evolution of the small family of alternative splicing modulators Nuclear Speckle RNA-binding proteins (NSRs) in plants. Genes 11, 207. doi: 10.3390/genes11020207.

Martínez de Alba A.E., Moreno A.B., Gabriel M., Mallory A.C., Christ A., Bounon R., Balzergue S., Aubourg S., Gautheret D., Crespi M.D., Vaucheret H., Maizel A. (2015). In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs. Nucleic Acids Research 43(5): 2902-2913.

Mejias, J., Bazin, J., Truong, N.M., Chen, Y., Marteu, N., Bouteiller, N., Sawa, S., Crespi, M.D., Vaucheret, H., Abad, P., Favery, B., and Quentin, M. (2021). The root-knot nematode effector MiEFF18 interacts with the plant core spliceosomal protein SmD1 required for giant cell formation. New Phytol 229, 3408-3423. doi: 10.1111/nph.17089.

Michaeli, S., Clavel, M., Lechner, E., Viotti, C., Wu, J., Dubois, M., Hacquard, T., Derrien, B., Izquierdo, E., Lecorbeiller, M., Bouteiller, N., De Cilia, J., Ziegler-Graff, V., Vaucheret, H., Galili, G., and Genschik, P. (2019). The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1. Proc Natl Acad Sci U S A 116, 22872-22883.

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(6):937-948. doi: 10.1016/j.molp.2021.03.008.

Moreno A.B., de Alba A.E.M., Bardou F., Crespi M.D., Vaucheret H., Maizel A., Mallory A.C. (2013). Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants. Nucleic Acids Research 41(8): 4699-4708.

Ohtani M, Kurihara Y, Seki M, Crespi M (2019) RNA-Mediated Plant Behavior. Plant Cell Physiol 60(9):1893-1896. doi: 10.1093/pcp/pcz168. 

Parent J.S., Bouteiller N., Elmayan T., Vaucheret H. (2015a). Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant Journal 81(2): 223-232.

Parent J.S., Jauvion V., Bouche N., Beclin C., Hachet M., Zytnicki M., Vaucheret H. (2015b). Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes. Nucleic Acids Research 43(17): 8464-8475.

Rigo R, Bazin J, Crespi M, Charon C (2019) Alternative Splicing in the Regulation of Plant-Microbe Interactions. Plant Cell Physiol pii: pcz086. doi: 10.1093/pcp/pcz086.

Rigo R*, Bazin J*, Romero-Barrios N, Moison M, Lucero L, Christ A, Benhamed M, Blein T, Huguet S, Charon C, Crespi M** and Ariel F** (*co-first authors, **co-corresponding authors) (2020) The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors. EMBO reports 21(5):e48977. doi: 10.15252/embr.201948977.

Rodriguez-Granados N.Y., Ramirez-Prado J.S., Veluchamy A., Latrasse D., Raynaud C., Crespi M., Ariel F., Benhamed M. (2016). Put your 3D glasses on: plant chromatin is on show. Journal of Experimental Botany 67(11): 3205-3221.

Romero-Barrios N, Legascue MF, Benhamed M, Ariel F, Crespi M (2018) Splicing regulation by long noncoding RNAs. Nucleic Acids Res 46(5):2169-2184 doi: 10.1093/nar/gky095.

Shamandi N., Zytnicki M., Charbonnel C., Elvira-Matelot E., Bochnakian A., Comella P., Mallory A.C., Lepere G., Saez-Vasquez J., Vaucheret H. (2015). Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. PLOS Biology 13(12): e1002326.

Swarup R., Crespi M., Bennett M.J. (2016). One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants. Developmental Cell 39(4): 383-385.

Taochy, C., Gursanscky, N.R., Cao, J., Fletcher, S.J., Dressel, U., Mitter, N., Tucker, M.R., Koltunow, A.M.G., Bowman, J.L., Vaucheret, H., and Carroll, B.J. (2017). A Genetic Screen for Impaired Systemic RNAi Highlights the Crucial Role of DICER-LIKE 2. Plant Physiol 175, 1424-1437.

Taochy, C., Yu, A., Bouche, N., Bouteiller, N., Elmayan, T., Dressel, U., Carroll, B.J., and Vaucheret, H. (2019). Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis. Nucleic Acids Res 47, 9104-9114.

Tran V.D.T., Souiai O., Romero-Barrios N., Crespi M., Gautheret D. (2016). Detection of generic differential RNA processing events from RNA-seq data. RNA Biology 13(1): 59-67.

Veluchamy A., Jégu T., Ariel F., Latrasse D., Mariappan K.G., Kim S.-K., Crespi M., Hirt H., Bergounioux C., Raynaud C., Benhamed M. (2016). LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLOS ONE 11(7): e0158936.

Van Du T., Souiai O., Romero-Barrios N., Crespi M. and Gautheret D. (2016) Detection of Generic Differential RNA Processing Events from RNA-seq Data. RNA Biology, 13(1):59-67.

Wu, Y.Y., Hou, B.H., Lee, W.C., Lu, S.H., Yang, C.J., Vaucheret, H., and Chen, H.M. (2017). DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. Plant J

Yu A., Saudemont B., Bouteiller N., Elvira-Matelot E., Lepere G., Parent J.S., Morel J.B., Cao J., Elmayan T., Vaucheret H. (2015). Second-Site Mutagenesis of a Hypomorphic argonaute1 Allele Identifies SUPERKILLER3 as an Endogenous Suppressor of Transgene Posttranscriptional Gene Silencing. Plant Physiology 169(2): 1266-1274.

Communications in conferences:

RNA workshop Arabidopsis Meeting, Vienna, Austria (F. Bardou selected oral pres., M. Crespi invited) July 2012

Cold Spring Harbor New York (J-S. Parent: selected oral pres.)

10th International Plant Molecular Biology Meeting, IPMB, Jeju, South Corea (M.Crespi invited) November 2012

Cold Spring Harbor Asia Epigenetics (F. Ariel: selected oral pres.) November 2012

Satellite to ASPB Meeting, Post-transcriptional regulation of Gene expression Workshop, Providence, USA (M. Crespi, invited speaker) July 2012

Non-coding RNA in Plants, Wittenberg, Germany (M. Crespi, invited speaker) July 2012

72nd Harden Conference RNA Regulators of Gene Expression (H Vaucheret, plenary speaker), Cambridge, UK, July 28-30, 2012

Cold Spring Harbor Asia Epigenetics (H Vaucheret, plenary speaker), October 29 – November 2, 2012

Conférence Jacques Monod RNA, key coordinator of gene expression (H Vaucheret, plenary speaker), October 7-11, 2012

Post-transcriptional regulation of Gene expression Workshop, Poznan, Polland (M. Crespi, invited speaker; Ariel F. selected oral pres.) September 2013

EMBO Meeting, Heidelberg (Ariel F., selected oral pres.) November 2013

EU COST meeting on Development of novel non-transgenic strategies for plant virus control (H Vaucheret, plenary speaker), Kandersteg, Suisse, May 13-14, 2013

Molecular Plant-Microbe Interactions symposium (H Vaucheret, plenary speaker), Taipei, Taiwan, October 3-4, 2013

EMBO|EMBL Symposium: Non-Coding Genome (Nahid Shamandi, short talk), Heidelberg, Allemagne, October 9-10, 2013

Workshop ARN non codants (H Vaucheret, plenary speaker), Paris, December 19, 2013

EFSA workshop Risk assessment considerations for RNAi-based GM plants (H Vaucheret, plenary speaker), Bruxelles, Belgique, June 4-5, 2014

Plant Post-transcriptional Gene Expression Regulation in Plants PGRP2015 (M. Crespi, invited speaker) Poznan, Polland, June 2014

Post-transcriptional Regulation of Gene expression in Plants, satellite workshop to ICAR 2015 (H. Vaucheret, plenary speaker), Paris, France, July 10-11, 2015, (M. Crespi President and Organizer)

The non-coding genome (M. Crespi, invited speaker), UPMC, Paris, 2015

ICAR 2015 (M. Crespi, invited speaker), Paris 2015

Cold Spring Harbor Asia Conference on RNA Biology (H. Vaucheret, plenary speaker), Suzhou, Chine, November 2016

Cold Spring Harbor Asia Conference on RNA Biology (M. Crespi, plenary speaker), Suzhou, Chine, November 2016

Induced Plant Development Meeting Cambridge, Sainsbury Lab (M. Crespi, plenary speaker), Cambridge, UK, April 2016

SPLICING 2016 (M. Crespi invited speaker), Caparica, Portugal, June 2016

Royal Society Symposium on Small RNA Pathways (H. Vaucheret, plenary speaker), Edinburgh, Scotland, March 2017

The short and the Long ncRNAs, (M. Crespi, invited speaker), Crete, Greece, June 2017

International Plant Molecular Biology (IPMB) congress (plenary speaker), Montpellier, France, August 2018

Plant Epigenetics meeting (plenary speaker), Strasbourg, February 2019

Tri-National Arabidopsis meeting (TRAM 11) (plenary speaker), Zurich, April 2019

Barcelona RNAclub 2nd meeting, (plenary speaker), Barcelona, June 2019

Modification date: 22 September 2023 | Publication date: 22 August 2012 | By: MJS