Systemic impact of small regulatory RNAs

Genetics, cell biology and development

MicroRNAs ("miRNAs") are small post-transcriptional regulators. The function of these small RNAs in animals has been well characterized at a molecular level, but their role is less well known at the macroscopic scale: how could miRNAs have any biological function if they repress most of their targets less than 2-fold (while inter-individual gene expression fluctuation typically exceeds 2-fold, and is buffered by homeostatic mechanisms)?
According to the current dogma, each miRNA regulates tens or hundreds of targets, yet several observations suggest miRNAs have a much weaker impact on animal biology. Our recent work also suggests that both experimental and computational miRNA target identification methods are heavily contaminated with false positives: these false positives may be truly repressed by miRNAs at the molecular scale, but such a small repressive effect fails to translate into a macroscopic phenotype for most genes.
Our work thus suggests that the biological role of miRNAs has been largely over-estimated. We are currently exploring practical consequences of this new theoretical framework, measuring the contribution of individual miRNA/target interactions to global in vivo phenotypes.
More generally, we are proposing a new vision of gene regulation: a regulatory target is not simply a gene that is affected by a regulatory pathway; it is a gene that is affected enough by the pathway – the extent of a measured regulation needs to be confronted to the robustness of biological systems to fluctuations.

figure 3 fr
BUSSEAU Isabelle
Gestionnaire parc binoculaires et injection



A rationalized definition of general tumor suppressor microRNAs excludes miR-34a

Sophie Mockly, Élisabeth Houbron, Hervé Seitz


Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5´ end of the siRNA guide strand

Vincent Brechin, Fumikazu Shinohara, Jun-Ichi Saito, Hervé Seitz, Yukihide Tomari


Re-assessment of the involvement of Snord115 in the serotonin 2C receptor pathway in a genetically relevant mouse model.

Hebras J, Marty V, Personnaz J, Mercier P, Krogh N, Nielsen H, Aguirrebengoa M, Seitz H, Pradere JP, Guiard BP, Cavaille J

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

Patricia Richard, Shuang Feng, Yueh-Lin Tsai, Wencheng Li, Paola Rinchetti, Ubayed Muhith, Juan Irizarry-Cole, Katharine Stolz, Lionel A Sanz, Stella Hartono, Mainul Hoque, Saba Tadesse, Hervé Seitz, Francesco Lotti, Michio Hirano, Frédéric Chédin, Bin Tian, James L Manley

Prospects and challenges of multi-omics data integration in toxicology.

Canzler S, Schor J, Busch W, Schubert K, Rolle-Kampczyk UE, Seitz H, Kamp H, von Bergen M, Buesen R, Hackermüller J

Inconsistencies and Limitations of Current MicroRNA Target Identification Methods.

Mockly S, Seitz H

Editorial: miRNA Regulatory Pathways in Metazoans. Advances From in vivo and ex vivo Studies.

Amar L, Seitz H

On the number of functional microRNA targets.

Seitz H

Functional lability of RNA-dependent RNA polymerases in animals.

Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop.

Buesen R, Chorley BN, da Silva Lima B, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermüller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann HM, Laffont M, McMullen P, Meehan R, Pemberton M, Perdichizzi S, Piersma AH, Sauer UG, Schmidt K, Seitz H, Sumida K, Tollefsen KE, Tong W, Tralau T, van Ravenzwaay B, Weber RJM, Worth A, Yauk C, Poole A

microRNA target prediction programs predict many false positives

Pinzon, N., Li, B., Martinez, L., Sergeeva, A., Presumey, J., Apparailly, F., Seitz, H

Issues in current microRNA target identification methods

Seitz H

Coding and non-coding variants in the SHOX2 gene in patients with early-onset atrial fibrillation

Hoffmann S, Clauss S, Berger IM, Weiß B, Montalbano A, Röth R, Bucher M, Klier I, Wakili R, Seitz H, Schulze-Bahr E, Katus HA, Flachsbart F, Nebel A, Guenther SP, Bagaev E, Rottbauer W, Kääb S, Just S, Rappold GA.

Advancing the use of noncoding RNA in regulatory toxicology: Report of an ECETOC workshop

Aigner A, Buesen R, Gant T, Gooderham N, Greim H, Hackermüller J, Hubesch B, Laffont M, Marczylo E, Meister G, Petrick JS, Rasoulpour RJ, Sauer UG, Schmidt K, Seitz H, Slack F, Sukata T, van der Vies SM, Verhaert J, Witwer KW, Poole A

Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner

Eckenfelder A, Ségéral E, Pinzón N, Ulveling D, Amadori C, Charpentier M, Nidelet S, Concordet JP, Zagury JF, Paillart JC, Berlioz-Torrent C, Seitz H, Emiliani S, Gallois-Montbrun S.

microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus

Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM

Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation

Royo H, Seitz H, ElInati E, Peters AH, Stadler MB, Turner JM

Cnidarian microRNAs frequently regulate targets by cleavage

Moran, Y., Fredman, D., Praher, D., Li Z. L., Meng Wee,L., Rentzsch, F., Zamore,P.D., Technau, U., Seitz H.

Quantitative aspects of RNA silencing in metazoans

Sergeeva, A., Restrepo, N.P., and Seitz, H.

Recognition of the pre-miRNA structure by Drosophila Dicer-1

Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y

A 5´-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation

Seitz H, Tushir JS, Zamore PD


Prospects and challenges of multi-omics data integration in toxicology.

Canzler S, Schor J, Busch W, Schubert K, Rolle-Kampczyk UE, Seitz H, Kamp H, von Bergen M, Buesen R, Hackermüller J
2020 - Arch Toxicol , 94(2):371-388 32034435
Service porteur : Systemic impact of small regulatory RNAs

The gastrula transition reorganizes replication origin selection in Caenorhabditis elegans

Rodríguez-Martínez, M., Pinzón, N., Ghommidh, C., Beyne, E., Seitz, H., Cayrou, C., Méchali, M.
2017 - Nature Structural & Molecular Biology , 24(3):290-299 28112731
Service porteur : Replication and Genome Dynamics

Insect small non-coding RNA involved in epigenetic regulations

Chambeyron, S., Seitz, H.
2014 - Current Opinion in Insect Science , 1, 1-19
Service porteur : Non-coding RNA, epigenetics and genome stability

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LI Blaise
LI Blaise
Institut Pasteur
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Comenius Unversity, Bratislava, Slovakia
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MAZE Delphine
MAZE Delphine
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PINZON Natalia
PINZON Natalia
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GATO Alexandre
GATO Alexandre
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Topic : Reciprocal repressions between microRNA and messenger RNA
Sophie MOCKLY 01/10/2017 - 31/12/2021
Thesis supervisor : Hervé SEITZ

Publications during the thesis :

1. Mockly S. et Seitz H. Inconsistencies and limitations of current microRNA target identification methods (2019) Methods Mol Biol, 1970:291-314 (lien Pubmed :

2. Mockly S., Houbron É et Seitz H. A rationalized definition of tumor suppressor microRNAs excludes miR-34a (soumis, manuscrit accessible à :


Mesurer la contribution d’interactions individuelles entre miARN et cible sur un phénotype in vivo

Le miARN bantam a été découvert par un crible génétique chez la Drosophile : les homozygotes mutants meurent au stade pupal précoce, les hétérozygotes sont plus petits que les sauvages, et les mouches surexprimant bantam sont plus grosses que les sauvages ; les hypomorphes sont partiellement stériles femelles (Hipfner et al., 2002). La première cible proposée pour bantam a été le gène proapoptotique hid, dont la 3´ UTR contient plusieurs sites de complémentarité à la graine de bantam (Brennecke et al., 2003). De nombreuses autres cibles ont été proposées (les programmes de prédiction de cibles prédisent ≈ 70 cibles avec des sites de complémentarité conservée à bantam), certaines d’entre elles sont réprimées par bantam de manière mesurable au niveau de l’abondance de la protéine ou de l’ARNm, mais aucune validation in vivo rigoureuse de l’implication d’une cible dans le phénotype de croissance, de létalité ou de stérilité n’a encore été apportée. Par exemple, la régulation du gène enabled par bantam est très claire d’après des expériences de gène-rapporteur (Becam et al., 2011), mais l’ablation génétique des sites de reconnaissance de bantam sur le gène endogène enabled ne semble pas perturber le patron d’expression d’enabled ou déclencher un phénotype particulier (Bassett et al., 2014).

Nous nous concentrerons donc sur une stratégie purement in vivo pour mesurer la contribution de cibles individuelles au phénotype bantam. Par édition du génome, nous avons préparé des mouches mutantes dont la graine de bantam a été mutée en un autre hexamère. Nous sommes actuellement en train de préparer des mouches mutantes où les sites de reconnaissance de bantam dans le gène hid ont été mutées de manière compensatoire, afin d’isoler la contribution de l’interaction bantam/hid au phénotype global contrôlé par bantam (de façon similaire à la stratégie décrite par Ecsedi et al., 2015).

figure 1
En mutant le miARN bantam in vivo, nous pouvons vérifier les phénotypes macroscopiques contrôlés par ce miARN. En mutant ses sites de reconnaissance sur une cible individuelle, nous pouvons évaluer la contribution de cette interaction particulière au phénotype global. En combinant les deux mutations compensatoires dans la même mouche, nous pouvons confirmer l’importance de cette interaction sur le phénotype in vivo.


Identifier les cibles de miR-34 qui contrôlent la prolifération cellulaire chez les Mammifères

La famille de miARN miR-34 suscite un très grand intérêt depuis qu’il a été proposé qu’elle contrôlait la prolifération cellulaire à la fois chez l’Homme et la Souris (He et al., 2007). De nombreuses cibles ont été proposées pour expliquer le contrôle de la prolifération par miR-34, sur la base d’expériences ex vivo, mais les preuves in vivo manquent toujours (Concepcion et al., 2012).

En utilisant un crible à haut débit, nous allons muter chaque site de fixation-candidat de miR-34 et mesurer l’effet de cette mutation sur la prolifération des cellules de Mammifères. Notre but consistera à identifier les cibles directes et indirectes de miR-34 qui affectent le plus fortement la prolifération cellulaire, et d’apporter une mesure précise de leur contribution à ce phénotype.

figure 2
En utilisant un crible à haut débit, nous identifierons les interactions individuelles miR-34/cible qui exercent le plus fort effet sur la prolifération cellulaire. Les mécanismes d’amplification et d’atténuation dans les réseaux régulateurs en aval seront identifiés par la mesure des perturbations d’expression des cibles indirectes.

Education and previous positions

2017: 5 year activity evaluation by the IGH (team “seniorized”, made permanent)
2011-2016: Junior group leader at the IGH
2009: HDR at the university Toulouse III Paul Sabatier
2005-2009: Postdoctoral fellow in Prof. Phillip Zamore’s laboratory, University of Massachusetts Medical School, Worcester (MA, USA)
2001-2004: PhD student in Dr. Jérôme Cavaillé’s laboratory (LBME, CNRS and université Toulouse III Paul Sabatier)
1997-2001: Undegraduate student at the École normale supérieure (rue d’Ulm, Paris)

Lab funding

2021 - 2024: ANR PRC, project "SCOuBiDou"

2020 - 2021: Fondation ARC « Projets »
2018 - 2021: CEFIC LRI « C5 »
2017: « Émergence » (Cancéropôle Grand Sud-ouest)
2012 - 2016: ATIP-Avenir (CNRS and Inserm, co-sponsored by Sanofi)
2010 - 2012: CDA (Human Frontier Science Program)

Expertise activities

Referee for scientific journals in the domains of RNA biology, bio-informatics, genomics and molecular genetics (Current BiologyEMBO ReportsGenome ResearchNucleic Acids ResearchRNA Biology, ...).
Referee for national and international grant agencies (ERC, SNF, HFSP, ANR, …).
Member of Cefic Long-range research initiative’s “Governance leadership team”.
Correction and authorship of notes for ANSES’ “Bulletin de veille scientifique”.

2021 issue of the InteRNAt summer school (November 2–6, 2021, in Sète):

Website of the event :

2019 issue of the InteRNAt summer school (October 6–10, 2019, in Sète):

Website of the event :

Content of the introductory lectures given during the first half-day of the summer school (in French)(introduction on RNAi, on microRNAs, and on the biochemistry of the RISC complex; exercises): freely downloadable here.

Collaborator Aim of the collaboration Common publications
Dr. Yukihide TOMARI
(université de Tõkyõ)
Web site
Analysis of structural determinants of microRNA biogenesis Kawamata et al. (2009)

Tsutsumi et al. (2011)
Dr. Ulrich TECHNAU
(université de Vienne)
Web site
Functional analysis of small regulatory RNAs in Nematostella vectensis Moran et al. (2014)
(SARS Center)
Web site
Functional analysis of small regulatory RNAs in Nematostella vectensis Moran et al. (2014)
Prof. Phillip D. ZAMORE
(école de médecine de
l'université du Massachusetts)
Web site
Functional analysis of small regulatory RNAs in Nematostella vectensis Moran et al. (2014)
Dr. James TURNER
(Crick Institute, Londres)
Web site
Analysis of the expression of microRNAs subjected to an epigenetic control in mammals Royo et al. (2015)
Dr. Denis TAGU
(INRA Rennes)
Web site
Characterization of small regulatory RNAs in pea aphid  
(IRMB, Montpellier)
Web site
Measurement of inter-individual fluctuation in gene expression in neutrophils Pinzón et al. (2017)
Dr. Marcel MÉCHALI
(IGH, Montpellier)
Web site
Identification of replication origins in early Nematode development and epigenetic characterization Rodríguez-Martínez et al. (2017)
Dr. Mark COCK
(UMR 8227, Roscoff)
Web site
MicroRNA identification in the brown alga Ectocarpus silicosus Tarver et al. (2015)
Prof. Gudrun RAPPOLD
(UniversitätKlinikum, Heidelberg)
Web site
Identification of a microRNA binding site specific to patients with atrial fibrillation Hoffmann et al. (2016)
Dr. Hector ESCRIVA
(Observatoire océanologique de Banyuls)
Web site
Characterization of small RNAs in the cephalochordate Branchiostoma lanceolatum

Marlétaz et al. (2018) Pubmed

Pinzón et al. (2019) Pubmed

(Institut Cochin, Paris)
Web site
Identification of Ago binding sites in HIV-1 viral RNA Eckenfelder et al. (2017)
Dr. James Manley
(Columbia university, New York, États-Unis)
Web site
Characterization of molecular consequences of SETX repression in human cells Richard et al. (2020) Pubmed 
Dr. Jérôme Cavaillé (CBI, Toulouse)
Web site

Evaluation of molecular and physiological consequences of the deletion of the SNORD115 RNA

Hebras et al. (2020) Pubmed

 GitHub repository

Manuscript "Mockly et al., 2022"

Manuscript “Pinzón et al., 2019”

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A Compressed fileB_lanceolatum_transcriptome_bowtie2_index.tar.bz2 152.04 MB
A Compressed fileBl71nemr.fa.bz2 128.94 MB
A file of unknown 2.67 KB
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A file of unknown typeConvincing_pre-miRNA_hairpins.fa 6.26 KB
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An Adobe Acrobat fileGel_purification_8h_embryos.pdf 9.57 MB
An Adobe Acrobat fileGel_purification_15h_embryos.pdf 9.6 MB
An Adobe Acrobat fileGel_purification_36h_embryos.pdf 11.19 MB
An Adobe Acrobat fileGel_purification_60h_embryos.pdf 10.16 MB
An Adobe Acrobat fileGel_purification_adult_females.pdf 9.09 MB
An Adobe Acrobat fileGel_purification_adult_males.pdf 8.48 MB
A file of unknown typeJunction_and_exonic_reads_blat_output.dat 172.2 KB
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A file of unknown typeOrthologs_to_known_hairpins.fa 3.29 MB
A file of unknown typeR_commands_convincing_ORF-matching_reads 1.89 KB
A file of unknown typeR_commands_genomic_non_ncRNA-matching_size_dist 1.36 KB
A file of unknown typeR_commands_hairpin-matching_size_dist 1.76 KB
A file of unknown typeR_commands_hairpin_read_profile 2.76 KB
A file of unknown typeR_commands_plot_miRNAs_in_dvpt 1.91 KB
A file of unknown typeR_commands_size_distribution_September2017 4.01 KB
A file of unknown typeR_commands_transcriptome_non_hairpin-matching_size_dist 1.87 KB
A file of unknown typeR_commands_worm_convincing_ORF-matching_size_dist 1.88 KB
A file of unknown typeR_commands_worm_extragenomic_extratranscriptomic_size_dist 1.33 KB
A file of unknown typeR_commands_worm_genomic_non_ncRNA-matching_size_dist 1.34 KB
A file of unknown typeR_commands_worm_hairpin-matching_size_dist 1.74 KB
A file of unknown typeR_commands_worm_transcriptome_non_hairpin-matching_size_dist 1.85 KB
A file of unknown typeR_commands_worm_transcriptomic_extragenomic_size_dist 1.77 KB
A file of unknown typeRdRP_template_loci.bed 168 bytes
A file of unknown 6.69 KB
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A file of unknown 1.03 KB
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A file of unknown typeStatistics.dat 1.08 KB
A file of unknown typeTop_antisense_junction_mapped_mRNAs.dat 0 bytes
A file of unknown typeTop_sense_junction_mapped_mRNAs.dat 314 bytes
A Compressed fileTranscripts_with_convicing_ORFs_in_Bla_annot_final_refTranscripts.fa.bz2 10.25 MB
A Compressed fileTrimmed_fastq.tar 2.44 GB
A file of unknown typeabundant_B_lanceolatum_ncRNAs.fa 521.74 KB
A Compressed fileblanc_evm+_rn.fa.bz2 7.72 MB
A Compressed fileblat_output.psl.bz2 657.3 MB
A file of unknown typecel_abundant_ncRNAs.fa 129.46 KB
A file of unknown typecel_hairpinMar18.fa 37.51 KB
A file of unknown typehairpinMar18.fa 5.85 MB
A Text filemd5sum_Seitz.txt 3.6 KB
A file of unknown typemiRNA_abundance_in_development.dat 7.08 KB
A file of unknown typeunified1.fa 1.1 MB

Manuscript "Mockly and Seitz, 2019"

Manuscript "Pinzón et al., 2017":

Scripts and data for the preparation of all 6 figures:

Cytometry FCS file to text file conversion:

Conversion script (usage : ./ input.fcs output.txt) : python script.

Context :

CNRS researchers have to submit every year a yearly activity report, and every 5 years they have to submit a “phased activity report” which is more detailed (as well as a “mid-phase activity report” in the middle of that 5 year-period). Following the merge of regions Midi-Pyrénées and Languedoc-Roussillon, laboratories in Languedoc-Roussillon joined the phase of Midi-Pyrénées laboratories, thus delaying by one year the evaluation which was scheduled for 2019 (it will take place in 2020).

In addition, laboratories are evaluated every 5 to 6 years by an international committee, which is assembled by HCERES (formerly known as AERES), which will then issue an evaluation report (in English).

Activity reports and evaluation reports for our team:

2020 evaluation report of our team by HCERES (in English)

2020 phased activitiy report of Hervé Seitz (January 2014 – December 2019) (in French)

2016 mid-phase activity report of Hervé Seitz (January 2014 – September 2016) (in French)

2014 evaluation report of our team by AERES (in English)

2014 phased activity report of Hervé Seitz (January 2009 – December 2013) (in French)

« La technologie CRISPR/Cas9 » 
(compte-rendu de la conférence donnée par Hervé Seitz au colloque « Quelles limites pour les technosciences en santé ? » à Clermont-Ferrand le 13 mars 2018, et publié dans le n°15 de la Revue du Centre Michel de l'Hospital).

Parallèle entre l'informatique et la génétique
(édition du génome, débuggage, matérialité de l'information, ...) (interview donnée dans le cadre des Tic-Talks du LIG).

Les statistiques en science expérimentale. Principe, limitations, erreurs courantes, illustrées par les rumeurs pseudo-scientifiques sur la Covid-19
(visio-conférence donnée le 13 mars 2021 sur invitation du cercle zététique du Languedoc-Roussillon ; diaporama cliquable accessible ici).

Outreach videos :

Open questions

Molecular biology explained to your grandmother