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.
1. Molecular identification of epigenetic targets of the RNAi machinery genome-wide
2. Subcellular architecture and trafficking dynamics of non-coding RNAs
1. Identification of epigenetic targets regulated by a specific novel RNAse III-like.
2. Identification of the function of 2 non-coding RNAs, APOLO and ASCO, affecting chromatin organisation and alternative splicing dynamic responses
1. Positional cloning of one epimutation and validation of a new methodology to generate epimutations.
2. Genome-wide analysis of the mechanism through which ncRNAs impact alternative splicing.
Publications (as of September, 2019):
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.
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.
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.
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.
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.
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.
Parent J.S., Bouteiller N., Elmayan T., Vaucheret H. (2015). 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. (2015). 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.
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.
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.
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.
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 14-18, 2016
Cold Spring Harbor Asia Conference on RNA Biology (M. Crespi, plenary speaker), Suzhou, Chine, November 14-18
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