Insulator dysfunction and oncogene activation in IDH mutant gliomas

Abstract

Gain-of-function IDH mutations are initiating events that define major clinical and prognostic classes of gliomas1,2. Mutant IDH protein produces a novel onco-metabolite, 2-hydroxyglutarate (2-HG), that interferes with iron-dependent hydroxylases, including the TET family of 5′-methylcytosine hydroxylases3–7. TET enzymes catalyze a key step in the removal of DNA methylation8,9. IDH mutant gliomas thus manifest a CpG island methylator phenotype (G-CIMP)10,11, though the functional significance of this altered epigenetic state remains unclear. Here we show that IDH mutant gliomas exhibit hyper-methylation at CTCF binding sites, compromising binding of this methylation-sensitive insulator protein. Reduced CTCF binding is associated with loss of insulation between topological domains and aberrant gene activation. We specifically demonstrate that loss of CTCF at a domain boundary permits a constitutive enhancer to aberrantly interact with the receptor tyrosine kinase gene PDGFRA, a prominent glioma oncogene. Treatment of IDH mutant gliomaspheres with demethylating agent partially restores insulator function and down-regulates PDGFRA. Conversely, CRISPR-mediated disruption of the CTCF motif in IDH wildtype gliomaspheres up-regulates PDGFRA and increases proliferation. Our study suggests that IDH mutations promote gliomagenesis by disrupting chromosomal topology and allowing aberrant regulatory interactions that induce oncogene expression.

Transcription organizes euchromatin similar to an active microemulsion

“…In the case of heterochromatin, which is transcriptionally repressed, organization can be explained by phase separation (Larson et al, 2017;Strom et al, 2017). For euchromatin, the transcriptionally permissive part of chromatin, spatial organization is required in development and health (Lupiáñez et al, 2015;Flavahan et al, 2016;Hnisz et al, 2016;Symmons et al, 2016), but a mechanism of euchromatin organization has not yet been described.…”

Oncometabolite Tinkers with Genome Folding, Boosting Oncogene Expression

“…Does altered CTCF binding perturb the 3D organisation of the genome and deregulate gene expression in IDH mutant cells? In support of this idea, the authors demonstrate that genes located in separate domains show more similar expression in IDH mutant cells than in IDH wild type cells [2]. Until high-resolution Hi-C data for IDH mutant cells become available, the precise relationship between altered CTCF binding, genome folding, and gene regulation in IDH mutant cells remains speculative.…”

“…A recent paper [2] adds a new twist to the story by demonstrating that IDH mutations affect the binding of the chromatin organiser protein CTCF, which demarcates domains of genome folding [3]. To illustrate the relationship between 3D chromatin domains and CTCF binding, Figure 1 shows high-resolution Hi-C data ( Figure 1A) and CTCF ChIPsequencing data ( Figure 1B) for the genomic region home to the known glioma oncogene, PDGFRA.…”

“…Loss of CTCF binding correlates with increased DNA methylation, and preferentially occurs at CTCF binding sites with motifs that contain CG dinucleotides as targets of DNA methylation [2]. DNA methylation may not be the only cause of altered CTCF binding in IDH mutant cells: At some sites at least, the reported increase in DNA methylation is smaller than the observed drop in CTCF binding [2], and increased DNA methylation does not explain the new CTCF binding In normal cells, genes in the same domain show more similar expression than genes located in separate domains, in part because they share access to gene regulatory elements [7]. In this way, spatial segmentation of the genome facilitates the regulation of gene expression.…”

“…Nevertheless, the available data show that in IDH mutant cells the PDGFRA promoter interacts with an enhancer near the FIPL1L gene, almost a million base pairs away (Figure1), and that PDGFRA expression is upregulated [2].…”