RÉSUMÉ
Un-physiological activation of hypoxia inducible factor (HIF) is an early event in most renal cell cancers (RCC) following inactivation of the von Hippel-Lindau tumor suppressor. Despite intense study, how this impinges on cancer development is incompletely understood. To test for the impact of genetic signals on this pathway, we aligned human RCC-susceptibility polymorphisms with genome-wide assays of HIF-binding and observed highly significant overlap. Allele-specific assays of HIF binding, chromatin conformation and gene expression together with eQTL analyses in human tumors were applied to mechanistic analysis of one such overlapping site at chromosome 12p12.1. This defined a novel stage-specific mechanism in which the risk polymorphism, rs12814794, directly creates a new HIF-binding site that mediates HIF-1α isoform specific upregulation of its target BHLHE41. The alignment of multiple sites in the HIF cis-acting apparatus with RCC-susceptibility polymorphisms strongly supports a causal model in which minor variation in this pathway exerts significant effects on RCC development.
Sujet(s)
Facteurs de transcription à motif basique hélice-boucle-hélice/métabolisme , Néphrocarcinome/génétique , Régulation de l'expression des gènes tumoraux , Prédisposition génétique à une maladie , Sous-unité alpha du facteur-1 induit par l'hypoxie/métabolisme , Polymorphisme de nucléotide simple , Allèles , Facteurs de transcription à motif basique hélice-boucle-hélice/génétique , Néphrocarcinome/diagnostic , Lignée cellulaire tumorale , Immunoprécipitation de la chromatine , Chromosomes humains de la paire 12/génétique , Cycline D1 , Étude d'association pangénomique , Cellules HeLa , Cellules HepG2 , Séquençage nucléotidique à haut débit , Humains , Sous-unité alpha du facteur-1 induit par l'hypoxie/génétique , Cellules MCF-7 , Locus de caractère quantitatif , Petit ARN interférent/génétique , Petit ARN interférent/métabolisme , Régulation positiveRÉSUMÉ
Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting â¼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.
Sujet(s)
Helicase/métabolisme , Régulation de l'expression des gènes au cours du développement , Complexe Mi-2/NuRD/métabolisme , Nucléosomes/génétique , Protéines de protozoaire/métabolisme , Assemblage et désassemblage de la chromatine , Dictyostelium/génétique , Dictyostelium/croissance et développement , Nucléosomes/métabolismeRÉSUMÉ
Clear cell renal cell carcinoma (ccRCC) is characterized by loss of function of the von Hippel-Lindau tumour suppressor (VHL) and unrestrained activation of hypoxia-inducible transcription factors (HIFs). Genetic and epigenetic determinants have an impact on HIF pathways. A recent genome-wide association study on renal cancer susceptibility identified single-nucleotide polymorphisms (SNPs) in an intergenic region located between the oncogenes MYC and PVT1. Here using assays of chromatin conformation, allele-specific chromatin immunoprecipitation and genome editing, we show that HIF binding to this regulatory element is necessary to trans-activate MYC and PVT1 expression specifically in cells of renal tubular origins. Moreover, we demonstrate that the risk-associated polymorphisms increase chromatin accessibility and activity as well as HIF binding to the enhancer. These findings provide further evidence that genetic variation at HIF-binding sites modulates the oncogenic transcriptional output of the VHL-HIF axis and provide a functional explanation for the disease-associated effects of SNPs in ccRCC.
Sujet(s)
Translocateur nucléaire du récepteur des hydrocarbures aromatiques/génétique , Néphrocarcinome/génétique , Régulation de l'expression des gènes tumoraux , Sous-unité alpha du facteur-1 induit par l'hypoxie/génétique , Tumeurs du rein/génétique , Polymorphisme de nucléotide simple , Protéines proto-oncogènes c-myc/génétique , Translocateur nucléaire du récepteur des hydrocarbures aromatiques/métabolisme , Sites de fixation , Néphrocarcinome/métabolisme , Néphrocarcinome/anatomopathologie , Chromatine/composition chimique , Chromatine/métabolisme , Immunoprécipitation de la chromatine , Chromosomes humains de la paire 8 , ADN intergénique/génétique , ADN intergénique/métabolisme , Éléments activateurs (génétique) , Prédisposition génétique à une maladie , Étude d'association pangénomique , Humains , Sous-unité alpha du facteur-1 induit par l'hypoxie/métabolisme , Tumeurs du rein/métabolisme , Tumeurs du rein/anatomopathologie , Liaison aux protéines , Protéines proto-oncogènes c-myc/métabolisme , ARN long non codant/génétique , ARN long non codant/métabolisme , Transduction du signal , Protéine Von Hippel-Lindau supresseur de tumeur/génétique , Protéine Von Hippel-Lindau supresseur de tumeur/métabolismeRÉSUMÉ
Hypoxia-inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. To address these questions, we deployed a recently developed chromosome conformation assay that enables simultaneous high-resolution analyses from multiple viewpoints. These assays defined specific long-range interactions between intergenic HIF-binding regions and one or more promoters of hypoxia-inducible genes, revealing the existence of multiple enhancer-promoter, promoter-enhancer, and enhancer-enhancer interactions. However, neither short-term activation of HIF by hypoxia, nor long-term stabilization of HIF in von Hippel-Lindau (VHL)-defective cells greatly alters these interactions, indicating that at least under these conditions, HIF can operate on preexisting patterns of chromatin-chromatin interactions that define potential transcriptional targets and permit rapid gene activation by hypoxic stress.
Sujet(s)
Sites de fixation , Chromatine/génétique , Chromatine/métabolisme , Biologie informatique/méthodes , Facteur-1 induit par l'hypoxie/métabolisme , Régions promotrices (génétique) , Algorithmes , Facteurs de transcription à motif basique hélice-boucle-hélice/métabolisme , Lignée cellulaire tumorale , Immunoprécipitation de la chromatine , Analyse de regroupements , Éléments activateurs (génétique) , Régulation de l'expression des gènes , Glycolyse , Séquençage nucléotidique à haut débit , Humains , Spécificité d'organe/génétique , Liaison aux protéines , Activation de la transcriptionRÉSUMÉ
A crucial step in the cellular adaptation to oxygen deficiency is the binding of hypoxia-inducible factors (HIFs) to hypoxia response elements (HREs) of oxygen-regulated genes. Genome-wide HIF-1α/2α/ß DNA-binding studies revealed that the majority of HREs reside distant to the promoter regions, but the function of these distal HREs has only been marginally studied in the genomic context. We used chromatin immunoprecipitation (ChIP), gene editing (TALEN) and chromosome conformation capture (3C) to localize and functionally characterize a 82 kb upstream HRE that solely drives oxygen-regulated expression of the newly identified HIF target gene PAG1. PAG1, a transmembrane adaptor protein involved in Src signalling, was hypoxically induced in various cell lines and mouse tissues. ChIP and reporter gene assays demonstrated that the -82 kb HRE regulates PAG1, but not an equally distant gene further upstream, by direct interaction with HIF. Ablation of the consensus HRE motif abolished the hypoxic induction of PAG1 but not general oxygen signalling. 3C assays revealed that the -82 kb HRE physically associates with the PAG1 promoter region, independent of HIF-DNA interaction. These results demonstrate a constitutive interaction between the -82 kb HRE and the PAG1 promoter, suggesting a physiologically important rapid response to hypoxia.
Sujet(s)
Protéines adaptatrices de la transduction du signal/génétique , Facteurs de transcription à motif basique hélice-boucle-hélice/métabolisme , Chromatine/métabolisme , Facteur-1 induit par l'hypoxie/métabolisme , Protéines membranaires/génétique , Éléments de réponse , Activation de la transcription , Protéines adaptatrices de la transduction du signal/biosynthèse , Animaux , Hypoxie cellulaire , Lignée cellulaire , Chromatine/composition chimique , Cellules HeLa , Humains , Protéines membranaires/biosynthèse , Souris , Souris de lignée C57BL , Phosphoprotéines/biosynthèse , Phosphoprotéines/génétique , Régions promotrices (génétique) , Transduction du signal , src-Family kinases/métabolismeRÉSUMÉ
BACKGROUND: Conditional deletion of the tumour suppressor gene Apc within the murine intestine results in acute Wnt signalling activation. The associated over-expression of a myriad of Wnt signalling target genes yields phenotypic alterations that encompass many of the hallmarks of neoplasia. Previous transcriptomic analysis aimed at identifying genes that potentially play an important role in this process, inferred the Hormonally upregulated Neu-associated kinase (HUNK/Mak-v/Bstk1) gene as a possible candidate. Hunk is a SNF1 (sucrose non fermenting 1)-related serine/threonine kinase with a proposed association with many different tumour types, including colorectal cancer. METHODS: Here we describe the generation of a novel Hunk kinase deficient mouse which has been used to investigate the involvement of Hunk-kinase activity in intestinal homeostasis and tumourigenesis. RESULTS: We show that in the morphologically normal intestine, Hunk-kinase negatively regulates epithelial cell proliferation. However, the increase in cell proliferation observed in the Hunk kinase deficient intestine is counteracted by increased cell migration, thereby maintaining intestinal homeostasis. Using qRT-PCR, we further demonstrate that Hunk is significantly over-expressed in Apc deficient / Wnt-signalling activated intestinal tissue. Using the classical intestinal tumourigenesis Apc (Min) mouse model we show that loss of Hunk-kinase activity significantly reduced tumour initiation rates in the small intestine. However, an accompanying increase in the size of the tumours counteracts the impact this has on overall tumour burden or subsequently survival. CONCLUSIONS: In the intestinal setting we demonstrate that Hunk has a role in normal intestinal proliferation and homeostasis and, although it does not alter overall survival rates, activity of this kinase does impact on tumour initiation rates during the early stages in tumourigenesis in the small intestine.
Sujet(s)
Muqueuse intestinale/métabolisme , Protein kinases/génétique , Protein kinases/métabolisme , Séquence d'acides aminés , Animaux , Séquence nucléotidique , Prolifération cellulaire , Transformation cellulaire néoplasique/génétique , Transformation cellulaire néoplasique/métabolisme , Modèles animaux de maladie humaine , Cellules souches embryonnaires/métabolisme , Femelle , Régulation de l'expression des gènes , Techniques de knock-down de gènes , Ciblage de gène , Locus génétiques , Mâle , Souris , Données de séquences moléculaires , Tumeurs/génétique , Tumeurs/métabolisme , Tumeurs/mortalité , Tumeurs/anatomopathologie , Protein kinases/déficit , Protein-Serine-Threonine Kinases , Charge tumorale , Régulation positive , Voie de signalisation WntRÉSUMÉ
Control of chromatin structure is crucial for multicellular development and regulation of cell differentiation. The CHD (chromodomain-helicase-DNA binding) protein family is one of the major ATP-dependent, chromatin remodeling factors that regulate nucleosome positioning and access of transcription factors and RNA polymerase to the eukaryotic genome. There are three mammalian CHD subfamilies and their impaired functions are associated with several human diseases. Here, we identify three CHD orthologs (ChdA, ChdB and ChdC) in Dictyostelium discoideum. These CHDs are expressed throughout development, but with unique patterns. Null mutants lacking each CHD have distinct phenotypes that reflect their expression patterns and suggest functional specificity. Accordingly, using genome-wide (RNA-seq) transcriptome profiling for each null strain, we show that the different CHDs regulate distinct gene sets during both growth and development. ChdC is an apparent ortholog of the mammalian Class III CHD group that is associated with the human CHARGE syndrome, and GO analyses of aberrant gene expression in chdC nulls suggest defects in both cell-autonomous and non-autonomous signaling, which have been confirmed through analyses of chdC nulls developed in pure populations or with low levels of wild-type cells. This study provides novel insight into the broad function of CHDs in the regulation development and disease, through chromatin-mediated changes in directed gene expression.
Sujet(s)
Helicase/métabolisme , Protéines de liaison à l'ADN/métabolisme , Dictyostelium/croissance et développement , Différenciation cellulaire , Assemblage et désassemblage de la chromatine , Protéines de liaison à l'ADN/génétique , Expression des gènes , Analyse de profil d'expression de gènes , Transduction du signal/génétique , TranscriptomeRÉSUMÉ
Micrococcal nuclease (MNase) is an endonuclease that cleaves native DNA at high frequency, but is blocked in chromatin by sites of intimate DNA-protein interaction, including nucleosomal regions. Protection from MNase cleavage has often been used to map transcription factor binding sites and nucleosomal positions on a single-gene basis; however, by combining MNase digestion with high--throughput, paired-end DNA sequencing, it is now possible to simultaneously map DNA-protein interaction regions across the entire genome. Biochemical and bioinformatic protocols are detailed for global mono-nucleosome positioning at ~160 bp spacing coverage, but are applicable to mapping more broadly or for site-specific binding of transcription factors at ~50 bp resolution.
Sujet(s)
Cartographie chromosomique/méthodes , Séquençage nucléotidique à haut débit/méthodes , Nucléosomes/génétique , Chromatine/génétique , Clivage de l'ADN , ADN des protozoaires/génétique , ADN des protozoaires/isolement et purification , Dictyostelium/génétique , Banque de gènes , Génome de protozoaire , Micrococcal nuclease/composition chimique , Analyse de séquence d'ADN/méthodesRÉSUMÉ
Dictyostelium discoideum is an exceptionally powerful eukaryotic model to study many aspects of growth, development, and fundamental cellular processes. Its small-sized, haploid genome allows highly efficient targeted homologous recombination for gene disruption and knock-in epitope tagging. We previously described a robust system for the generation of multiple gene mutations in Dictyostelium by recycling the Blasticidin S selectable marker after transient expression of the Cre recombinase. We have now further optimized the system for higher efficiency and, additionally, coupled it to both, knock-out and knock-in gene targeting, allowing the characterization of multiple and cooperative gene functions in a single cell line.