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Doctorat De L'université De Toulouse En vue de l'obtention du DOCTORAT DE L'UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (Toulouse INP) Discipline ou spécialité : Pathologie, Toxicologie, Génétique et Nutrition Présentée et soutenue par : Mme MARIA EUGENIA MARTI MARIMON le vendredi 9 novembre 2018 Titre : 3D genome conformation and gene expression in fetal pig muscle at late gestation Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : Génétique, Physiologie et Systèmes d'Elevage (GenPhySE) Directeur(s) de Thèse : MME MARTINE YERLE M. SYLVAIN FOISSAC Rapporteurs : M. FREDERIC BANTIGNIES, CNRS Mme CAROLE CHARLIER, UNIVERSITE DE LIEGE Membre(s) du jury : M. OLIVIER GADAL, CNRS TOULOUSE, Président Mme MARTINE YERLE, INRA TOULOUSE, Membre M. SYLVAIN FOISSAC, INRA TOULOUSE, Membre Acknowledgments I would like in first place to express my gratitude to the members of the jury for the time they spent evaluating this work. Thanks to Dr. Carole Charlier and Dr. Frédéric Bantignies for agreeing to be the reviewers of this thesis and for their kind and helpful feedback on my thesis. I would like to thank also to Dr. Olivier Gadal and Dr. Roderic Guigo for accepting to be part of the thesis committee. Je voudrais remercier tout spécialement mes trois encadrants. Merci Martine d’avoir accepté d’encadrer cette thèse et de t’être rendue disponible quand j’en avais besoin malgré toutes tes responsabilités. Merci aussi d’avoir veillé à ce que cette thèse ait bien été menée à terme. Sylvain, un grand merci pour toute ton aide, tes conseils et ta patience. Oui, il a fallu l’être avec cette thésarde débutante en bioinfo dont tu as hérité. Mais surtout, Sylvain, merci pour ton optimisme et pour avoir su me remonter le moral dans les moments difficiles. Enfin, Yvette, je te remercie beaucoup pour tous ces échanges dans nos bureaux qui ont fait naitre des questions et des idées qui ont permis d’améliorer mon travail, ainsi que pour ces petits coups de pouce pour les manips (j’ai adoré travailler avec toi au labo). D’autres personnes ont énormément contribué à mon travail et je leur en serai toujours reconnaissante. Tout particulièrement Nathalie V., merci à toi pour ton aide inestimable dans toutes les analyses biostatisiques, sans lesquelles ce travail n’aurait pas été possible. Malgré ta charge de travail, tu as toujours su trouver le temps pour m’aider. Je voudrais aussi remercier Pierre Neuvial, responsable du projet SCALES qui a servi à financer une bonne partie du séquençage permettant d’améliorer la qualité de mes données. Merci également Laurence L. pour nos échanges et pour ton implication dans mon premier article, j’ai vraiment apprécié de collaborer avec toi. Sarah, merci pour tous ces petits coups de main et pour ta gentillesse. Hervé, tu as été présent dans la plupart des moments clés de mon parcours à l’INRA depuis mon arrivée. Tu as été la toute première personne rencontrée, et qui de plus parlait l’espagnol!). C’est en partie grâce à toi que je me suis inscrite au master, que j’ai prolongé mon CDD avec Alain V. (merci à toi aussi), et que ce projet a vu le jour (je me souviens encore de cette réunion improvisée au patio avec Sylvain où nous avons établi les bases de cette thèse). Sans votre aide, je ne serais pas là aujourd’hui en train d’écrire ces lignes. Merci bien sûr à tous les membres de mon équipe Cytogène pour votre accueil chaleureux et votre soutien. Enfin, merci à Florence M., David R., Matthias Z., Diane E., Noémie T., Lisa B., Katia F., Nicolas M. et tous ceux que j’ai pu oublier pour leurs petites mais précieuses contributions. La vie au labo n’aurait pas été la même sans « mes filles adorées », Manu, Lisa, Laure, Nathalie M. et Sonia, ainsi que sans toi Valentin (une petite pensée pour toi, même si tu as quitté le labo il y a longtemps). Yvette et Sylvain, je reviens à vous car plus qu’encadrants, vous êtes devenus de chers amis sur le plan personnel. Merci à tous pour tous ces moments partagés non seulement au travail mais aussi en soirées, vacances, etc., je vous porterai toujours dans mon cœur. Sachez que ces petites pauses- cigarette au patio avec vous les filles ainsi qu’avec Pitou, Yann, David, Sylvain, Juliette… vont énormément me manquer. Enfin un grand merci en général à tous les membres du ex-LGC qui depuis mon arrivée m’ont fait me sentir comme chez moi et qui, pour une étrangère comme moi, sont devenus une grande famille. A tous mes amis, spécialement aux « Toulousanos », et à ma famille un très grand merci; aux premiers pour me donner l’envie de rester en France, et pour me distraire et/ou me supporter quand la thèse devenait difficile; et à la deuxième, pour son aide inconditionnelle. ”Gràcies mamà i papà, per tota la vostra ajuda i per creure sempre en mi: Si és que tinc la sort de tindre els millors pares del món! Ana i Dani gràcies també a vosaltres per estar sempre a l’escolta encara que la distància no ens permeta parlar més sovint”. Enfin, en dernier, mais le plus important, Stéphane, je ne pourrais pas trouver tous les mots nécessaires pour te remercier mais je vais essayer... Depuis le début tu as été toujours à mes côtés, pour les bons mais aussi pour les mauvais moments. Tu as souffert pour moi plus que moi-même dans mes plus grandes périodes de stress et tu t’es réjoui et senti fier de moi à chaque petit succès que j’ai pu avoir. Sans jamais lâcher et toujours prêt à m’aider et à me faire sourire, je ne peux pas imaginer un meilleur compagnon dans ma vie. Table of contents 1 Abstract ................................................................................................................ 11 2 General introduction ........................................................................................... 13 3 Bibliographic review ........................................................................................... 17 3.1 Chapter 1. Breeding context ..................................................................................... 17 3.1.1 Early mortality: a major breeding issue in pig farming ....................................... 17 3.1.1.1 Background ................................................................................................. 17 3.1.1.2 Selection towards prolificacy ...................................................................... 17 3.1.1.3 Critical factors of piglets mortality ............................................................. 19 3.1.2 Maturity and survival ........................................................................................... 19 3.1.2.1 Critical factors for piglets survival ............................................................. 19 3.1.2.2 Piglet’s maturity .......................................................................................... 21 3.1.3 The role of muscle maturity in survival at birth ................................................... 21 3.1.3.1 Myogenesis: the fetal skeletal muscle development ................................... 21 3.1.3.2 Peculiarities of pig skeletal myogenesis and muscle metabolism .............. 25 3.1.3.3 Muscle and maturity ................................................................................... 27 3.2 Chapter 2. Muscle transcriptome studies ................................................................. 29 3.2.1 Functional Annotation of porcine genome ........................................................... 29 3.2.1.1 Main efforts in pig genome sequencing and annotation ............................. 29 3.2.2 Transcriptome technologies and approaches ........................................................ 31 3.2.2.1 DNA microarray and RNA-seq .................................................................. 31 3.2.2.2 Co-expression networks .............................................................................. 33 3.2.3 Muscle transcriptome studies in pigs ................................................................... 35 3.3 Chapter 3. Nuclear architecture ................................................................................ 37 3.3.1 Higher order genome organization ....................................................................... 37 3.3.1.1 Generalities ................................................................................................. 37 3.3.1.2 Chromosome territories .............................................................................. 39 3.3.1.3 NPCs, LADs, NADs, TFs and PcG domains .............................................. 41 3.3.1.4 A and B compartments ................................................................................ 43 3.3.1.5 Topologically associated domains .............................................................. 45 3.3.2 Chromatin loops and gene-gene interactions ....................................................... 49 3.3.2.1 CTCF and cohesin functions ....................................................................... 49 3.3.2.2 Insulated neighborhoods (CTCF/cohesin-mediated loops) ........................ 49 3.3.2.3 Gene-gene interactions ................................................................................ 51 3.3.3 Dynamic organization of the genome .................................................................. 55 3.3.4 Single cell genome organization .......................................................................... 57 3.3.5 3D genome architecture and disease .................................................................... 57 3 3.3.6 3D genome architecture
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