Unicentre CH-1015 Lausanne http://serval.unil.ch RRRYear : 2016 Transcriptional programs during mammalian cell prolifération Rib Leonor Rib Leonor, 2016, Transcriptional programs during mammalian cell prolifération Originally published at : Thesis, University of Lausanne Posted at the University of Lausanne Open Archive http://serval.unil.ch Document URN : urn:nbn:ch:serval-BIB_51F1A1F006D84 Droits d’auteur L'Université de Lausanne attire expressément l'attention des utilisateurs sur le fait que tous les documents publiés dans l'Archive SERVAL sont protégés par le droit d'auteur, conformément à la loi fédérale sur le droit d'auteur et les droits voisins (LDA). A ce titre, il est indispensable d'obtenir le consentement préalable de l'auteur et/ou de l’éditeur avant toute utilisation d'une oeuvre ou d'une partie d'une oeuvre ne relevant pas d'une utilisation à des fins personnelles au sens de la LDA (art. 19, al. 1 lettre a). 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Centre Intégratif de Génomique Transcriptional programs during mammalian cell proliferation Thèse de doctorat ès sciences de la vie (PhD) présentée à la Faculté de biologie et de médecine de l’Université de Lausanne par Leonor Rib Informaticien diplômée par l’Universitat Politècnica de Catalunya, Espagne Jury Dr. Werner Held, President, Université de Lausanne, Switzerland Dr. Winship Herr, Thesis supervisor, Université de Lausanne, Switzerland Dr. Nicolas Guex, Thesis co-supervisor, Swiss Institute of Bioinformatics, Switzerland Dr. Philipp Bucher, Expert, École polytechnique fédérale de Lausanne, Switzerland Dr. Liliane Michalik, Expert, Université de Lausanne, Switzerland Dr. Ueli Schibler, Expert, Université de Genève, Switzerland Lausanne, 2016 Abstract Gene transcription is a precise and complex process that initiates the expression of the genetic code. Transcription of genes can lead to highly coordinated cellular processes such as cell proliferation and eventually to physiological changes such as mouse liver regeneration. RNA polymerases are the major enzymes involved in transcription and their action is regulated by different elements that bind to the chromatin and modify its activity. Host Cell Factor 1 (HCF-1) is one case of a transcriptional co-regulator. The HCF-1 precursor protein is proteolytically cleaved for its maturation into two subunits (HCF-1N and HCF-1C) that remain bound non- covalently and become active. The mature HCF-1 regulates transcription via chromatin association with transcription factors and chromatin remodelers in gene promoters. Furthermore, HCF-1 is required for proper progression of mammalian cell division, especially for the passage from G1 to S phase and for proper mitosis. The advent of high-throughput sequencing technologies in the past ten years has permitted transcriptional studies at a genome-wide scale. A genome-wide study of HCF-1 showed that it is a common component of active CpG-island promoters and coincides with the occupancy of the transcription factors ZNF143, THAP11, YY1 and GABP. In this dissertation, I show novel insights about the genome-wide regulation of mammalian transcription in cancerous and differentiated cells. Initially I evaluate the use of paired-end sequencing to study genome-wide binding of transcription regulators to the chromatin. This technology proves to have advantages compared to the traditional single-end sequencing. Subsequently, I report new insights about the chromatin binding of HCF- 1 along the cell division of HeLa cells. In the CDC6 promoter, paired-end sequencing revealed two HCF-1 binding sites with different underlying DNA motifs associated to the transcription factors E2F1 and THAP11/ZNF143. This suggests that HCF-1 could bind to the chromatin through different transcription factors in the same promoter. Interestingly, the individual association with these transcription factors appears to vary during the course of the cell cycle. In this work, I also investigate transcription regulation in the mouse liver. I initially characterize the genome-wide transcriptional responses to partial hepatectomy in the mouse liver, showing that the mouse liver undergoes two different transcriptional cycles: a sham-like cycle and second cycle linked to cell proliferation. Additionally, I describe that the genic accumulation of H3K36me2 in the regenerating mouse liver and in HeLa cells accumulates at the 5’ end of transcriptional units whereas H3K36me3 accumulates towards the 3’ end. This observation was already reported only in Drosophila which suggests potential similar mechanisms for Pol2 elongation. And lastly, I show that HCF-1 in the mouse liver is a versatile component for the regulation of genes involved in diverse cellular functions in which the two HCF- 1 subunits display different chromatin associations. i Résumé pour le grand public Nos cellules comportent chacune deux séries d’instructions que nous avons héritées de nos parents. Ces instructions sont compactées de façon remarquable pour tenir dans la très petite taille du noyau cellulaire. Ceci est en parti réalisé en enroulant la séquence d’ADN autour de protéines appelées histones, formant la chromatine. Cependant, les cellules possèdent divers mécanismes de régulation pour la lecture des instructions, appelée transcription. Ceci implique la participation d’ARN polymérases (les lecteurs), ainsi que d’autres facteurs de régulation comme des co-activateurs ou des co-répresseurs, par exemple Host Cell Factor 1 (HCF- 1). Ils coexistent tous avec des facteurs de remodelage de la chromatine qui peuvent lire et modifier les marques épigénétiques sur les histones. Au début du 21ème siècle, de nouvelles technologies ont été mises au point pour permettre la visualisation de la position de ces tous petits éléments sur l’ensemble des gènes contenus dans les cellules. Cette révolution dans les sciences du vivant contribue à élucider les mécanismes de régulation de la transcription lors de processus cellulaires tels que la division cellulaire. Dans ce manuscrit, je présente différents modèles de régulation de la transcription des gènes que j’ai observés en étudiant les positions de régulateurs. J’ai pu étudier ceci dans deux types de cellules : a) des cellules humaines cancéreuses qui se multiplient constamment et b) des cellules saines du foie de souris. Le foie est un organe possédant une capacité de régénération remarquable. Lorsqu’il est lésé, il a la capacité de multiplier les cellules restantes pour restaurer sa masse et sa fonction. Lors de la régénération, j’ai observé que les ARN polymérases peuvent lire les gènes rapidement ou lentement selon le besoin. De plus, la position des marques épigénétiques H3K36me2 et H3K36me3 lors de la régénération donne des pistes sur le mécanisme de lecture. J’ai également étudié le rôle du cofacteur de transcription HCF-1. A la fois dans les cellules cancéreuses et dans les cellules du foie, HCF-1 est une protéine polyvalente qui peut agir différemment d’un promoteur à l’autre. HCF-1 est de plus impliqué dans la lecture de gènes associés à des fonctions cellulaires très variées. Ceci en fait une protéine très intéressante à étudier, puisqu’elle permet d’obtenir des pistes sur différents modes de régulation. En conclusion, bien que les deux séries d’instructions reçues de nos parents soient statiques, les éléments qui interagissent avec elles sont extrêmement divers et dynamiques, et agissent de manière précise pour que les cellules réalisent leurs fonctions lorsque nécessaire. Une meilleure compréhension de cette diversité et de cette précision permettra dans le futur d’aider à concevoir de meilleures drogues pour traiter les maladies. ii Acknowledgements During these five years of doctoral studies I have been fortunate to have the support and teachings of some people that I would like to acknowledge here. First, I would like to acknowledge Winship Herr, my supervisor, for accepting the challenge to teach a computer scientist on how to do research in molecular biology during these five years, and for even accepting that I conducted my own research in the wet lab. I appreciate very much his teachings on the value of doing good science and the transparency with which he does science as this has also given me the opportunity to develop many complementary soft skills. I would also like to thank Nicolas Guex, my co-supervisor. I would like to thank him for his availability during these five years, his teachings and his motivation. The collaboration with him has been very interesting and creative. I would like to thank all the members of the lab for their support, teachings and friendship. I would like to specially thank Dominic Villeneuve, who from the first moment has been very inspiring to me. He answered all the questions I asked him regularly about biology and experiments, and I was very fortunate to have him supervising most of my experimental research making it a very inspiring and exciting scientific experience. I would also like to thank Viviane Praz, because she has always been available to answer my questions. I learned a lot from our discussions that often took longer than expected. I would also like to especially thank Laura Sposito, as I have found it very easy to collaborate with her. I would like to particularly thank her for the long discussions and support while I did my experimental research, and for her friendship in the difficult moments.