Systemic impact of small regulatory RNAs

Genetics, cell biology and development

• Team
• PhD theses
• Projects
• Members
• Publications
• Biography
• Alumni
• InteRNAt summer school on eukaryotic small regulatory RNAs
• Collaborators
• Slides of seminars given in public lecture
• Computer programs
• Tutorials
• Activity reports and evaluation
• Pour le grand public

https://www.igh.cnrs.fr/uploads/media/5e397fdb6b74d/impact-systemique-petits-arn.jpg

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.
 

BUSSEAU Isabelle
Gestionnaire parc binoculaires et injection
Researcher

SEITZ Herve
Researcher

HOUBRON Elisabeth
IT

MOCKLY Sophie
PhD Student

PUBLICATIONS OF THE TEAM

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

Published the 05/10/2020 - Elife , 9 33016258

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

Published the 18/07/2020 - Autophagy , DOI: 10.1080/15548627.2020.1796292 32686621

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.

Published the 09/02/2020 - Arch Toxicol 32034435

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.

Published the 10/04/2019 - Methods Mol Biol , 1970:291-314 30963499

Mockly S, Seitz H

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

Published the 20/03/2019 - Front Genet , 10:147 30886628

Amar L, Seitz H

On the number of functional microRNA targets.

Published the 10/03/2019 - Mol Biol Evol 30851114

Seitz H

Functional lability of RNA-dependent RNA polymerases in animals.

Published the 20/02/2019 - PLoS Genet , 15(2):e1007915 30779744

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

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Published the 23/11/2018 - Nature 30464347

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.

Published the 30/09/2017 - Regul Toxicol Pharmacol , 91 Suppl 1:S3-S13 28958911

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

Published the 01/01/2017 - Genome Res , 27, 2, 234-245 28148562

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

Issues in current microRNA target identification methods

Published the 01/01/2017 - RNA Biol , 1-4 28430005

Seitz H

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

Published the 01/01/2016 - Basic Res Cardiol , 111(3):36 27138930

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

Published the 01/01/2016 - Regul Toxicol Pharmacol. , 82, 127-139 27663666

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

Published the 01/01/2016 - Nucleic Acids Res , 45, 7, 4158-4173 28003477

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

Published the 01/01/2015 - Nucleic Acids Res , 43, 13, 6384-6398 26101255

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

Published the 01/01/2015 - PLoS Genet , 11(10):e1005461 26509798

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

Cnidarian microRNAs frequently regulate targets by cleavage

Published the 01/01/2014 - Genome Research , 24(4):651-63 24642861

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

Published the 01/01/2013 - Biochemistry (Mosc) , 78(6):613-26 23980888

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

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

Published the 01/01/2011 - Nat Struct Mol Biol , 18(10):1153-1158 21926993

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

Published the 01/01/2011 - Silence , 2:4 21649885

Seitz H, Tushir JS, Zamore PD

PUBLICATIONS COMMUNES

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 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

MARTINEZ Laura

send a message

GASPAROVA Iveta
Comenius Unversity, Bratislava, Slovakia

send a message

MAZE Delphine

send a message

PINZON Natalia

send a message

KONISHI Hideaki

send a message

BUSTO Germain
CHU de Montpellier

send a message

GATO Alexandre

send a message

SERGEEVA Anna

send a message

MARTIN Pierre

send a message

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 : https://pubmed.ncbi.nlm.nih.gov/30963499/)

2. Mockly S., Houbron É et Seitz H. A rationalized definition of tumor suppressor microRNAs excludes miR-34a (soumis, manuscrit accessible à : https://www.biorxiv.org/content/10.1101/2021.02.11.430795v4)

• Gene regulation vs. homeostasis: the microRNA case (PhD project offered for 2021)
• Mesurer la contribution d’interactions individuelles entre miARN et cible sur un phénotype in vivo
• Identifier les cibles de miR-34 qui contrôlent la prolifération cellulaire chez les Mammifères

 

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

(Yousra Mermat et Isabelle Busseau)

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).

 

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

(Sophie Mockly)

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.

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 Biology, EMBO Reports, Genome Research, Nucleic Acids Research, RNA 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 : https://internat21.sciencesconf.org/.

Pre-registration open from June 7, 2021 to July 25, 2021.

 

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

Website of the event : https://internat.sciencesconf.org.

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) Pubmed Tsutsumi et al. (2011) Pubmed
Dr. Ulrich TECHNAU (université de Vienne) Web site	Functional analysis of small regulatory RNAs in Nematostella vectensis	Moran et al. (2014) Pubmed
Dr. Fabian RENTZSCH (SARS Center) Web site	Functional analysis of small regulatory RNAs in Nematostella vectensis	Moran et al. (2014) Pubmed
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) Pubmed
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) Pubmed
Dr. Denis TAGU (INRA Rennes) Web site	Characterization of small regulatory RNAs in pea aphid
Dr. Florence APPARAILLY (IRMB, Montpellier) Web site	Measurement of inter-individual fluctuation in gene expression in neutrophils	Pinzón et al. (2017) Pubmed
Dr. Marcel MÉCHALI (IGH, Montpellier) Web site	Identification of replication origins in early Nematode development and epigenetic characterization	Rodríguez-Martínez et al. (2017) Pubmed
Dr. Mark COCK (UMR 8227, Roscoff) Web site	MicroRNA identification in the brown alga Ectocarpus silicosus	Tarver et al. (2015) Pubmed
Prof. Gudrun RAPPOLD (UniversitätKlinikum, Heidelberg) Web site	Identification of a microRNA binding site specific to patients with atrial fibrillation	Hoffmann et al. (2016) Pubmed
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
Dr. Sarah GALLOIS-MONTBRUN (Institut Cochin, Paris) Web site	Identification of Ago binding sites in HIV-1 viral RNA	Eckenfelder et al. (2017) Pubmed
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

• November 8, 2021 or the Small RNA Bioinformatics club : 30 minutes slideshow (speaker: Hervé Seitz); video record of the conference: link.
• November 8, 2021 or the Small RNA Bioinformatics club : 8 minutes slideshow (speaker : Sophie Mockly) ; video record of the conference : link.
• October 5, 2021 for Master 2 students in ecology at the university of Montpellier: 3h slideshow (speaker: Hervé Seitz)
• April 21, 2021 for the Cancéropôle Grand Sud-Ouest (Axis 2): 25 minutes slideshow (speaker: Hervé Seitz)
• March 13, 2021 for the association "Cercle zététique du Languedoc-Roussillon" (Montpellier, France): 2h slideshow (speaker: Hervé Seitz)
  Video record of the conference (in French): conference; questions/answers with the audience.
• February 2, 2021 at the CRCT Cancer research center of Toulouse: 50 minute slideshow (speaker: Hervé Seitz)
• September 28, 2020, for Master 2 students in ecology at the university of Montpellier: 4h30 slideshow (speaker: Hervé Seitz)
• November 28, 2019 at the colloquium Santé et droit de choisir (Clermont-Ferrand, France): 30 minute slideshow (in French) (speaker: Hervé Seitz).
• October 17, 2019 for the Visiatome (Marcoule, France): 1h slideshow (speaker: H. Seitz)
• May 15, 2019 for the association "Rando, Loisirs, Culture" (Grabels, France): 2h slideshow (speaker: Hervé Seitz)
• April 10, 2019 for the M1 masters students of Montpellier university : 15 minute slideshow (speaker: Hervé Seitz)
• January 23, 2019 at the Université du Tiers Temps (Montpellier, France): 50 minute slideshow (speaker: Hervé Seitz)
• January 16, 2019 at the Université du Tiers Temps (Montpellier, France): 50 minute slideshow (speaker: Hervé Seitz)
• November 23, 2018 at the Young Life Scientist meeting (Montpellier, France): 15 minute slideshow (speaker: Hervé Seitz)
• November 21, 2018 at the Journées Cancéropôle Grand Sud-Ouest (la Grande-Motte, France): 15 minute slideshow (speaker: H. Seitz)
• November 7, 2018 at the 11^th SifrARN meeting (Nancy, France): 25 minute slideshow (speaker: H. Seitz)
• October 19, 2018 at the colloquium on Artificial intelligence in biology and health (Montpellier, France) : 30 minute slideshow (speaker: H. Seitz)
• April 25, 2018 at the "Café des sciences" (Avignon, France): 15 minute slideshow (in French) (speaker: H. Seitz)
• March 13, 2018 at the colloquium Quelles limites pour les technosciences en santé ? (Clermont-Ferrand, France): 30 minute slideshow (in French) (speaker: H. Seitz).
• February 8, 2018 at the International course on Non-coding genome of Curie institute (Paris, France): 1h slideshow (speaker: H. Seitz).
• May 16, 2017 at the Colloque inter-LabEx CRISPR-Cas9 (Montpellier, France) : 15 minute slideshow (speaker: H. Seitz).
• June 27, 2016 at the Tõkyõ ncRNA symposium "Clues to non-coding RNA taxonomy" (Tõkyõ, Japon) : 15 minute slideshow (speaker: H. Seitz).
• March 3, 2016 at the ECETOC Workshop "ncRNAs and Risk Assessment Science" (Málaga, Spain): 15 minute slideshow (speaker: H. Seitz).
• February 20, 2017 at the Université du Tiers Temps (Montpellier, France): 1h slideshow (speaker : Isabelle Busseau)
• February 12, 2016 at the SMPGD (Statistical methods for post genomic data) annual workshop (Lille, France): 45 minute slideshow (speaker : H. Seitz).
• January 25, 2016 at the Keystone Symposium "Small RNA Silencing: Little Guides, Big Biology (A6)" (Keystone, U.S.): 12 minute slideshow (speaker : N. Pinzón).
• January 15, 2016 for the Centre d'éthique contemporaine de Montpellier : 1h slideshow (speaker : Isabelle Busseau)
• June 4, 2015 at the ESPE Science School "Non-coding RNAs in paediatric endocrinology" (Annecy, France): 30 minute slideshow (speaker : H. Seitz).
• June 9, 2014 at the Taiwan-France mini-symposium on regulatory RNAs (Taipei, Taïwan) : 40 minute slideshow (speaker: H. Seitz).
• February 27, 2014 for the L2 students in philosophy at the university Montpellier III: 1h slideshow (speaker: Isabelle Busseau)
• February 2, 2014 at the Keystone Symposium "RNA silencing (A9)" (Seattle, U.S.): 12 minute slideshow (speaker : H. Seitz).
• November 26, 2013 at the symposium Statistical analysis of RNA-seq data: advances and challenges of Pasteur institute (Paris, France): 45 minute slideshow (speaker : H. Seitz).
• March 22, 2013 at the Keystone Symposium "RNA silencing (C7)" (Whistler, Canada): 12 minute slideshow (speaker: H. Seitz).
• December 11, 2012 at the International course on Non-coding genome of Curie institute (Paris, France): 1h slideshow (speaker : H. Seitz).
• October 13, 2012 at the BTCure miRNA workshop (Montpellier, France): 30 minute slideshow (speaker : H. Seitz).
• September 12, 2012 at the Annual French conference on Drosophila (Clermont-Ferrand, France): 30 minute slideshow (speaker : H. Seitz).
• August 30, 2012 at the Cold Spring Harbor Laboratory Meeting "Regulatory and Non-coding RNAs" (Cold Spring Harbor, U.S.):  15 minute slideshow (speaker : N. Pinzón).
• April 24, 2012 at the Schlumberger Foundation conference "Small Silencing RNA Biology and Mechanism" (Tourtour, France): 1h slideshow (speaker: H. Seitz).
• June 15, 2011 at the Sixteenth annual meeting of the RNA society (Kyōto, Japan): 12 minute slideshow (speaker: H. Seitz).
• June 13, 2011 at the Tōkyō RNA club symposium (Tōkyō, Japan): 15 minute slideshow (speaker: H. Seitz).
• June 10, 2011 at the Fifth annual Arthropod genomics symposium (Kansas City, U.S.): 30 minute slideshow (speaker: H. Seitz).
• December 2, 2010 at the Fifth European workshop on immune-mediated inflammatory diseases (Sitges, Spain): 30 minute slideshow (speaker: H. Seitz).
• May 19, 2009 at the Microsymposium on small RNAs (Vienna, Austria): 30 minute slideshow (speaker: H. Seitz).

 GitHub repository

Manuscript “Pinzón et al., 2019”

Predicted animal proteome sequence download

Filename	Size
00_Proteome_download.md	12.65 KB
All_predicted_proteomes.tar.bz2	3.31 GB
Available_at_Ensembl.txt	3.09 KB
Module_measures_proteome_size_dist.pl	485 bytes
Protein_lengths_in_predicted_proteomes.tar.bz2	19.55 MB
R_commands_statistics_on_protein_lengths	1.1 KB
Species_with_at_least_1000_proteins_of_more_than_1000aa.txt	8.35 KB
Species_with_at_least_5000_proteins_of_more_than_500aa.txt	7.21 KB
genomes_overview.txt	53.05 KB

Search for RdRP candidates and re-sequencing of the "BL09445" locuslocus “BL09945”

Filename	Size
01_RdRP_search.md	10.65 KB
Clone4.fa	2.87 KB
Clone5.fa	2.89 KB
Every_PFAM_RdRP_evening_hitdata_concise.txt.bz2	178.25 KB
Every_PFAM_RdRP_evening_hitdata_full.txt.bz2	1.7 MB
Every_PFAM_RdRP_evening_hitdata_standard.txt.bz2	459.97 KB
Fuses_lines_clean.pl	514 bytes
Order_11104254864-1_Results.zip	9.08 MB
Order_11104283914-1_Results.zip	7.77 MB
R_commands_piecharts	352 bytes
RdRP_profiles.tar.bz2	650.82 KB
Sequences_candidates_every_PFAM_RdRP.fa.bz2	816.88 KB

Phylogeny of the "eukaryotic RdRP" protein family

Filename	Size
02_RdRP_phylogeny.md	1.49 KB
Cipres_DataMARSV1short3MBLG.zip	77.66 MB
RDRPMARSV1alignHMMALIGNShortV3TRIM.fasta	206.61 KB
RdRPMARSV1.fa	467.16 KB
STDERR	0 bytes
STDOUT	1.25 MB
_JOBINFO.TXT	347 bytes
_scheduler_stderr.txt	634 bytes
done.txt	49 bytes
infile.nex.bz2	80.16 KB
infile.nex.ckp.bz2	83.41 KB
infile.nex.ckp7E.bz2	83.35 KB
infile.nex.con.tre.bz2	36.9 KB
infile.nex.mcmc.bz2	10.85 KB
infile.nex.parts.bz2	11.96 KB
infile.nex.run1.p.bz2	113.92 KB
infile.nex.run1.t.bz2	33.64 MB
infile.nex.run2.p.bz2	113.8 KB
infile.nex.run2.t.bz2	33.34 MB
infile.nex.trprobs.bz2	625.68 KB
infile.nex.tstat.bz2	8 KB
infile.nex.vstat.bz2	30.3 KB
paramfile.txt	61 bytes
scheduler.conf	65 bytes
start.txt	40 bytes
stderr.txt	0 bytes
stdout.txt	1.25 MB
term.txt	318 bytes

Small RNA-Seq in Branchiostoma lanceolatum

Filename	Size
03_Small_RNA-Seq.md	29.47 KB
B_lanceolatum_genome_bowtie2_index.tar.bz2	776.93 MB
B_lanceolatum_transcriptome_bowtie2_index.tar.bz2	152.04 MB
Bl71nemr.fa.bz2	128.94 MB
Chef3.sh	2.67 KB
Chef4.sh	2.92 KB
Convincing_pre-miRNA_hairpins.fa	6.26 KB
Fuses_lines_clean.pl	514 bytes
Gel_purification_8h_embryos.pdf	9.57 MB
Gel_purification_15h_embryos.pdf	9.6 MB
Gel_purification_36h_embryos.pdf	11.19 MB
Gel_purification_60h_embryos.pdf	10.16 MB
Gel_purification_adult_females.pdf	9.09 MB
Gel_purification_adult_males.pdf	8.48 MB
Junction_and_exonic_reads_blat_output.dat	172.2 KB
Module_ORF_detector.pl	2.01 KB
Module_ORF_detector_lower_case.pl	2.04 KB
Module_TXT_to_FA.pl	513 bytes
Module_converts_fastq_to_fasta.pl	539 bytes
Module_excludes_hairpin-matching_reads.pl	1.42 KB
Module_extract_from_fasta.pl	572 bytes
Module_extract_from_fastq.pl	671 bytes
Module_extracts_fastq_read_identifiers.pl	349 bytes
Module_extracts_miRNA_hairpins.pl	1.35 KB
Module_extracts_read_sequences.pl	748 bytes
Module_logo_for_hairpin-matching.pl	1.89 KB
Module_selects_from_blat_results.pl	4.35 KB
Module_unification.pl	1.7 KB
Orthologs_to_known_hairpins.fa	3.29 MB
R_commands_convincing_ORF-matching_reads	1.89 KB
R_commands_genomic_non_ncRNA-matching_size_dist	1.36 KB
R_commands_hairpin-matching_size_dist	1.76 KB
R_commands_hairpin_read_profile	2.76 KB
R_commands_plot_miRNAs_in_dvpt	1.91 KB
R_commands_size_distribution_September2017	4.01 KB
R_commands_transcriptome_non_hairpin-matching_size_dist	1.87 KB
R_commands_worm_convincing_ORF-matching_size_dist	1.88 KB
R_commands_worm_extragenomic_extratranscriptomic_size_dist	1.33 KB
R_commands_worm_genomic_non_ncRNA-matching_size_dist	1.34 KB
R_commands_worm_hairpin-matching_size_dist	1.74 KB
R_commands_worm_transcriptome_non_hairpin-matching_size_dist	1.85 KB
R_commands_worm_transcriptomic_extragenomic_size_dist	1.77 KB
RdRP_template_loci.bed	168 bytes
Script_C_elegans.sh	6.69 KB
Script_convincing_transcriptome-matching_not_matching_ncRNA_or_hairpins.sh	315 bytes
Script_mapping_extragenomic_on_RdRP_template_loci.sh	713 bytes
Script_mapping_on_RdRP_template_loci.sh	1.03 KB
Script_miRNAs_in_development.sh	5.38 KB
Script_transcriptome-matching_not_matching_ncRNA_or_hairpins.sh	1.05 KB
Statistics.dat	1.08 KB
Top_antisense_junction_mapped_mRNAs.dat	0 bytes
Top_sense_junction_mapped_mRNAs.dat	314 bytes
Transcripts_with_convicing_ORFs_in_Bla_annot_final_refTranscripts.fa.bz2	10.25 MB
Trimmed_fastq.tar	2.44 GB
abundant_B_lanceolatum_ncRNAs.fa	521.74 KB
blanc_evm+_rn.fa.bz2	7.72 MB
blat_output.psl.bz2	657.3 MB
cel_abundant_ncRNAs.fa	129.46 KB
cel_hairpinMar18.fa	37.51 KB
hairpinMar18.fa	5.85 MB
md5sum_Seitz.txt	3.6 KB
miRNA_abundance_in_development.dat	7.08 KB
unified1.fa	1.1 MB

Pathogen and potential pathogen-matching reads

Filename	Size
04_Pathogen_and_potential_pathogen_matching_reads.md	24.99 KB
ATCV1_contig_mappers.tar.bz2	1.91 KB
ATCV1_genome.fa	285.38 KB
All_medium_and_long_contigs.xml.bz2	13.94 MB
Chef.sh	1.36 KB
Chef2.sh	971 bytes
Chef_ATCV1.sh	1.3 KB
Contig_name_correspondance.txt	3.99 MB
Module_parse_XML.pl	1.67 KB
R_commands_ATCV1_size_dist	750 bytes
R_commands_contig_length_statistics	99 bytes
R_commands_legended_mapping_on_contig	1.74 KB
R_commands_mapping_on_bacterial_genomes	1.73 KB
R_commands_mapping_on_contig	1.74 KB
R_commands_mapping_on_viral_contig	1.28 KB
R_commands_mapping_on_viral_contig_all_stages_together	1.5 KB
R_commands_mapping_on_viral_genome	1.74 KB
R_commands_pathogenic_bacteria_size_dist	810 bytes
R_commands_top_contig_size_dist	815 bytes
Staphylococcus_aureus_genome.fa.bz2	783.99 KB
Unified_contigs.fa	3.06 MB
Vibrio_alginolyticus_genome.fa.bz2	1.41 MB
Vibrio_anguillarum_genome.fa.bz2	1.12 MB
Viral_contigs.fa	600 bytes

Manuscript "Mockly and Seitz, 2019"

• Scripts and data for the preparation of Table 1:
  Mockly_and_Seitz_Table1.tar.bz2

Manuscript "Pinzón et al., 2017":

• Comparison of miR-223-guided repression amplitude to inter-individual variability in target gene expression: source code and data files.
• Absolute quantification of mRNAs in C2C12 cells during differentiation: source code and data files.
• High-throughput comparison of gene dose-sensitivity and miRNA binding site conservation: source code and data files.

Scripts and data for the preparation of all 6 figures:

• Figure_1.tar.bz2
• Figure_2.tar.bz2
• Figure_3.tar.bz2
• Figure_4.tar.bz2
• Figure_5.tar.bz2
• Figure_6.tar.bz2

Cytometry FCS file to text file conversion:

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

1. Unix training

• First lecture: browsing the arborescence, manipulating files, tricks and advice, redirecting to a file, grep, combining commands
• Second lecture: the nano text editor, writing and executing scripts, sedSecond lecture: the nano text editor, writing and executing scripts, sed

2. Statistics in molecular biology

Introductory statistics for biologists

3. R training

• First lecture: basic commands
• Second lecture: tracing graphs
• Third lecture: a few statistical tests
• Fourth lecture: a few advanced commands

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).