Transcriptional programs during mammalian cell prolifération

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. -- 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

Differential regulation of RNA polymerase III genes during liver regeneration.

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand

Rapid Recapitulation of Nonalcoholic Steatohepatitis upon Loss of Host Cell Factor 1 Function in Mouse Hepatocytes

Host-cell factor 1 (HCF-1), encoded by the ubiquitously expressed X-linked gene Hcfc1, is an epigenetic coregulator important for mouse development and cell proliferation, including during liver regeneration. We used a hepatocyte-specific inducible Hcfc1 knock-out allele (called Hcfc1 <sup>hepKO</sup> ), to induce HCF-1 loss in hepatocytes of hemizygous Hcfc1 <sup>hepKO/Y</sup> males by four days. In heterozygous Hcfc1 <sup>hepKO/+</sup> females, owing to random X-chromosome inactivation, upon Hcfc1 <sup>hepKO</sup> allele induction, a 50/50 mix of HCF-1 positive and negative hepatocyte clusters is engineered. The livers with Hcfc1 <sup>hepKO/Y</sup> hepatocytes displayed a 21-24-day terminal non-alcoholic fatty liver (NAFL) followed by non-alcoholic steatohepatitis (NASH) disease progression typical of severe NAFL disease (NAFLD). In contrast, in livers with heterozygous Hcfc1 <sup>hepKO/+</sup> hepatocytes, HCF-1-positive hepatocytes replaced HCF-1-negative hepatocytes and revealed only mild-NAFL development. Loss of HCF-1 led to loss of PGC1α protein, probably owing to its destabilization, and deregulation of gene expression particularly of genes involved in mitochondrial structure and function, likely explaining the severe Hcfc1 <sup>hepKO/Y</sup> liver pathology. Thus, HCF-1 is essential for hepatocyte function, likely playing both transcriptional and non-transcriptional roles. These genetically-engineered loss-of-HCF-1 mice can be used to study NASH as well as NAFLD resolution

Discovery of TeV γ-ray emission from the neighbourhood of the supernova remnant G24.7+0.6 by MAGIC

SNR G24.7+0.6 is a 9.5 kyrs radio and gamma-ray supernova remnant evolving in a dense medium. In the GeV regime, SNR G24.7+0.6 (3FHL J1834.1– 0706e/FGES J1834.1–0706) shows a hard spectral index (Γ∼2) up to 200 GeV, which makes it a good candidate to be observed with Cherenkov telescopes such as MAGIC. We observed the field of view of SNR G24.7+0.6 with the MAGIC telescopes for a total of 31 hours. We detect very high energy γ-ray emission from an extended source located 0.34 degree away from the center of the radio SNR. The new source, named MAGIC J1835–069 is detected up to 5 TeV, and its spectrum is well-represented by a power-law function with spectral index of 2.74 ± 0.08. The complexity of the region makes the identification of the origin of the very-high energy emission difficult, however the spectral agreement with the LAT source and overlapping position at less than 1.5 sigma point to a common origin. We analysed 8 years of Fermi-LAT data to extend the spectrum of the source down to 60 MeV. Fermi-LAT and MAGIC spectra overlap within errors and the global broad band spectrum is described by a power-law with exponential cutoff at 1.9 ± 0.5 TeV. The detected γ-ray emission can be interpreted as the results of proton-proton interaction between the supernova and the CO-rich surrounding

All-sky Medium Energy Gamma-ray Observatory: Exploring the Extreme Multimessenger Universe

The All-sky Medium Energy Gamma-ray Observatory (AMEGO) is a probe class mission concept that will provide essential contributions to multimessenger astrophysics in the late 2020s and beyond. AMEGO combines high sensitivity in the 200 keV to 10 GeV energy range with a wide field of view, good spectral resolution, and polarization sensitivity. Therefore, AMEGO is key in the study of multimessenger astrophysical objects that have unique signatures in the gamma-ray regime, such as neutron star mergers, supernovae, and flaring active galactic nuclei. The order-of-magnitude improvement compared to previous MeV missions also enables discoveries of a wide range of phenomena whose energy output peaks in the relatively unexplored medium-energy gamma-ray band

A cut-off in the TeV gamma-ray spectrum of the SNR Cassiopeia A

It is widely believed that the bulk of the Galactic cosmic rays is accelerated in supernova remnants (SNRs). However, no observational evidence of the presence of particles of PeV energies in SNRs has yet been found. The young historical SNR Cassiopeia A (Cas A) appears as one of the best candidates to study acceleration processes. Between 2014 December and 2016 October, we observed Cas A with the MAGIC telescopes, accumulating 158 h of good quality data. We derived the spectrum of the source from 100 GeV to 10 TeV. We also analysed 3c8 yr of Fermi-LAT to obtain the spectral shape between 60 MeV and 500 GeV. The spectra measured by the LAT and MAGIC telescopes are compatible within the errors and show a clear turn-off (4.6\u3c3) at the highest energies, which can be described with an exponential cut-off at E_c = 3.5(^{+1.6}_{-1.0})_{stat} (^{+0.8}_{-0.9})_{sys} TeV. The gamma-ray emission from 60 MeV to 10 TeV can be attributed to a population of high-energy protons with a spectral index of 3c2.2 and an energy cut-off at 3c10 TeV. This result indicates that Cas A is not contributing to the high energy ( 3cPeV) cosmic ray sea in a significant manner at the present moment. A one-zone leptonic model fails to reproduce by itself the multiwavelength spectral energy distribution. Besides, if a non-negligible fraction of the flux seen by MAGIC is produced by leptons, the radiation should be emitted in a region with a low magnetic field (B\u2a85180 \u3bcG) like in the reverse shock

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article