The healthy development of a living cell requires precise spatial-temporal gene expression. The code that dictates when and where genes are expressed is stored in a pattern of specific sequence motifs, which can be recognised by transcription factors. Understanding the interaction between these DNA sequence motifs and transcription factors will help to elucidate how genomic sequences build transcriptional control networks. However, the DNA-binding specificities of ~1400 human transcription factors are largely unknown. The in vivo DNA-binding events of transcription factors involve great subtlety, because most transcription factors recognise degenerate sequence motifs and related transcription factors often prefer similar or even identical sequences. Forkhead transcription factors exemplify these challenges. To understand how members within the Forkhead transcription factor family gain their binding and functional specificities, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) to interrogate the genome-wide chromatin binding events of three Forkhead transcription factors: FOXM1, FOXO3 and FOXK2. We find that FOXM1 specifically binds to the promoters of a large array of genes whose activities peak at the G2 and M phases of the cell cycle. The canonical Forkhead consensus GTAAACA is not enriched within the FOXM1 cistrome. It gains its own specific binding events and biological functions by interacting and cooperating with the MMB complex. FOXO3 and FOXK2 are recruited to chromatin by the canonical Forkhead consensus GTAAACA, and they bind both shared and specific regions in the genome. FOXO3 mostly binds to the regions which are also bound by FOXK2, but no competitive or assisted binding between FOXO3 and FOXK2 is detected within those regions. Overall, these results help explain how individual members of the Forkhead transcription factor family gain binding specificity within the genome yet raises new questions of how functional specificity is achieved by other family members.

Les modifications post-traductionnelles telles que la phosphorylation, l’OGlcNAcylation et l’ubiquitination jouent des rôles critiques dans la coordination des fonctions protéiques et par conséquent influencent grandement de nombreux processus cellulaires. Il est à noter que ces modifications sont hautement dynamiques et finement regulées. Par exemple, l’ubiquitination peut être réversible via l’action des déubiquitinases comme le suppresseur de tumeurs BAP1. Parmis les gènes codant pour les déubiquitinases, BAP1 est la plus souvent mutée dans le cancer. Des études récentes ont démontré l’importance des dynamiques de modifications post-traductionnelles dans la régulation du complexe BAP1. En plus, BAP1 forme un complexe multi-protéiques contenant plusieurs régulateurs transcriptionnels comme la protéine polycomb OGT et les facteurs de transcription FOXK1 et FOXK2. OGT est une enzyme unique qui catalyze l’ajout d’un groupement O-GlcNAc sur ses substrats afin d’en moduler l’activité enzymatique, les interactions protéines-protéines et leur localisation cellulaire. Cette modification est aussi liée au métabolisme puisque son substrat donneur, l’UDP-GlcNAc, est dérivé de la voie biosynthétique des hexosamines. Parallèlement, FOXK1/2 ont aussi été démontrés comme étant critiques à des processus métaboliques telles que la myogenèse et l’autophagie. Lors de nos études, nous avons identifié FOXK1 comme un nouveau substrat d’OGT. De plus, les niveaux d’O-GlcNAcylation de FOXK1 fluctuent lors de l’entrée/sortie du cycle cellulaire. En outre, nous avons identifié l’importance de FOXK1 dans l’adipogenèse et observé que l’interaction FOXK1/BAP1 est affectée par le métabolisme cellulaire. En résumé, nos études ont révélé l’importance d’OGT dans la régulation de certaines composantes du complexe BAP1, ce qui aidera à la compréhension de l’effet suppresseur de tumeur de BAP1 ainsi que son mécanisme d'action dans différents processus tel que le remodelage de la chromatine. / Post-translational modifications such as phosphorylation, O-GlcNAcylation and ubiquitination play critical roles in coordinating protein function and are therefore involved in diverse cellular processes. Of relevance here, ubiquitination may be removed by deubiquitinases such as the tumour suppressor BAP1, which represents the most mutated deubiquitinase gene in the human genome. Recent studies have revealed that important and dynamic post-translational modifications regulate several functions of the BAP1 complex. Indeed, BAP1 has been shown to form a multi-protein complex with several transcriptional regulators including the polycomb group protein OGT and the transcription factors FOXK1 and FOXK2. OGT is a unique enzyme that catalyzes the addition of an O-GlcNAc moiety to target proteins, which impacts protein function including enzymatic activity, protein-protein interactions and subcellular localization. This modification is also highly linked to cellular metabolism, as the donor substrate for the reaction, UDP-GlcNAc, is derived from the hexosamine biosynthesis pathway. Similarly, FOXK1 and FOXK2 have been shown to be implicated in metabolic processes such as myogenesis and autophagy. During our studies, we identified FOXK1 but not FOXK2 as a novel substrate of OGT. Further, we found that this OGlcNAcylation is modulated during the entry/exit of cell cycle. We also found that FOXK1 is critical for adipogenesis and that the interaction between FOXK1/BAP1 is compromised during nutrient starvation. Thus, our studies have revealed that OGT selectively modulates and regulates components of the BAP1 complex which may impact different cellular processes, notably chromatin remodelling and could help understanding how BAP1 acts as a tumor suppressor.