This work shows that the germline-specific CTCFL (BORIS) is aberrantly activated in high-grade serous ovarian carcinoma, where it remodels transcriptional, epigenetic, and three-dimensional genome organization by occupying CTCF-bound chromatin loop anchors and weakening CTCF-mediated chromatin insulation.
Abstract
Disruption of three-dimensional genome architecture is a major driver of cancer initiation and progression, frequently arising from genetic and epigenetic alterations at CTCF- and cohesin-bound chromatin anchors. These same chromatin loop anchors can also be occupied by the germ cell-specific CTCF paralog CTCFL (BORIS), which is aberrantly activated in multiple malignancies. Here, we show that in ovarian cancer cells, BORIS activation establishes a distinct transcriptional program that collapses following loss of BORIS chromatin binding and is accompanied by widespread changes in CTCF and cohesin occupancy, histone modifications, and chromatin accessibility. These BORIS-dependent transcriptional alterations occur in long-range genomic clusters, resulting in the coordinated activation or repression of neighboring genes, including hormonally regulated gene families. BORIS loss also increases topologically associating domain (TAD) insulation, strengthens A/B compartment segregation and chromatin loop interactions, and results in a more compact and constrained chromatin architecture. Together, our findings suggest that aberrant BORIS activation promotes transcriptional reprogramming by weakening CTCF-mediated chromatin insulation and relaxing three-dimensional genome organization in ovarian cancer. Significance High-grade serous ovarian carcinoma, the most common subtype of ovarian cancer, remains one of the deadliest gynecological malignancies because of its late diagnosis, extensive genomic instability, and frequent therapeutic resistance. The lack of reliable biomarkers for early detection underscores the need to identify new molecular drivers of disease initiation and progression. Here, we show that the germline-specific gene CTCFL (BORIS) is aberrantly activated in high-grade serous ovarian carcinoma, where it remodels transcriptional, epigenetic, and three-dimensional genome organization by occupying CTCF-bound chromatin loop anchors and weakening CTCF-mediated chromatin insulation. These findings identify BORIS as a key regulator of transcriptional reprogramming in ovarian cancer and support its further investigation as both a prognostic biomarker and a potential therapeutic target.
X-chromosome inactivation involves chromosome-wide gene silencing accompanied by extensive chromatin changes, as well the loss of topologically associating domains. Yet discrete regions of the inactive X chromosome retain activity within localised 3D domains, which contain active genes that variably escape from X inactivation. The transcription factor and architectural protein CTCF has been proposed to be implicated in escape by insulating escape domains or sustaining their topology via cohesin-mediated loop extrusion. Here, we test the role of CTCF and cohesin in escape using acute degron-mediated depletion of CTCF and RAD21 in neural progenitor cells with established escape profiles. Although CTCF occupancy correlates with escape status on the inactive X chromosome, its removal - together with loss of loop extrusion - does not disrupt escapee gene expression, or domain organization, nor does it result in spreading of silencing or activation of genes in cis. Rather, we show that facultative escape regions are self-sustaining compartments of active chromatin enriched in H3K27 acetylation and depleted in H3K27 methylation, with the magnitude of compartment strength scaling up with the degree of transcriptional activity on the inactive X chromosome. These active escapee compartments are propagated independently of CTCF and RAD21-dependent 3D architecture. Our findings identify chromatin compartmentalization as the primary feature of facultative escapee domains.
Antonia Hauth, A. Loda, Nikolai S. Bykov et al.· bioRxiv· 0 citations
A conserved role of CTCF is supported in preventing DNA methylation spreading and gene silencing of cell-type-specific genes along differentiation, and a similar role of CTCF on DNA methylation and gene expression in the human orthologous gene HBA2.
Gustavo Tapia-Urzúa, H. N. Núñez-Martínez, Sylvia Garza-Manero et al.· Epigenetics· 0 citations
CCCTC-binding factor (CTCF) is a key architectural protein in the three-dimensional (3D) genome, yet how its loss reshapes chromatin structure and transcription at single-cell resolution remains unclear. Using HiRES, which jointly profiles chromatin contacts and RNA from the same nucleus, we examined genome-wide effects of CTCF depletion. Topologically associating domain (TAD)–like domains (TLDs) across single cells remained largely unchanged in number and size after CTCF loss, but their boundaries became more variably positioned, and pseudobulk analyses revealed reduced interactions within A compartments. We also developed SALTAFinder to identify Spatially Aggregated Long-distance TLD Assemblies (SALTAs), clusters of TLDs occupying shared 3D space within single cells. A subset of SALTAs is enriched for highly expressed genes and super-enhancers and declines upon CTCF depletion. This structural reorganization coincided with a global reduction in per-cell RNA output, as indicated by HiRES and orthogonal measurements. Together, these findings suggest that CTCF contributes to the coordinated regulation of chromatin organization and transcriptional capacity and is associated with stabilization of long-range active chromatin clusters.
Zi-Yin Chen, Xuan-Yu Li, Yun-Peng Dai et al.· Science Advances· 0 citations
Extrachromosomal DNA (ecDNA) is a major driver of cancer pathogenesis, however, its spatial organization in the nucleus is not currently understood. Here we show that ecDNAs, in contrast to chromosomal DNA, preferentially localize to the nuclear periphery yet resist peripheral gene silencing. Single-molecule multi-omic sequencing and imaging-based CRISPR screening demonstrate enhanced ecDNA hub formation, H3K27ac and H3K9me3 bivalency, late DNA replication, long-range CpG hypomethylation, and increased transcriptional output when ecDNAs localize to the nuclear periphery. EcDNA anchors to the nuclear lamina through H3K9me3-dependent interactions with the Lamin B Receptor (LBR), which if interrupted, results in inward migration of ecDNA particles, reduced ecDNA congregation, and decreased transcription of ecDNA-encoded genes. These results reveal inherent advantages of the spatial organization of ecDNA that are not available to chromosomal DNA, enhancing ecDNA congregation and amplifying oncogenic transcriptional output, by localizing to the nuclear periphery of cancer cells.
Yan-Bo Wang, Xiao-Wei Yan, Natasha E. Weiser et al.· bioRxiv· 0 citations
Lineage-determining transcription factors (TFs), such as p63 in epithelial tissues, establish normal tissue identity but can also drive carcinogenesis. The epigenetic basis for these divergent effects, however, is unclear. Here, we show that p63 reorganizes three-dimensional (3D) chromatin topology in squamous cell carcinoma (SCC) through cooperation with the tumor-selective partner TF, FOXK1. Multi-omic profiling across normal and malignant states reveals that p63 enhances connectivity between cis-regulatory elements near oncogenes and promotes a secondary enhancer looping architecture, in which p63 and FOXK1-enriched enhancers indirectly contact target promoters via FOXK1-associated intermediate anchors lacking p63 binding. FOXK1 mediates p63-dependent chromatin looping, as FOXK1 loss selectively weakens p63-dependent loops and reduces transcription of associated target genes. The p63–FOXK1 interaction is observed in human tumor samples but not in normal tissues. Together, our findings define an epigenetic mechanism by which a lineage master TF and tumor-restricted partner TF reshape 3D chromatin structure to drive oncogenic transcription, with implications for tumor cell identity and therapy.
N. Jung, V. Lopez-Pajares, L. Donohue et al.· Science Advances· 0 citations
A comprehensive synthesis of the mechanisms and functional roles of classical chromatin remodelers within both physiological and neoplastic contexts is provided and a hierarchical framework that distinguishes between 'first-level' and 'higher-order' chromatin remodeling is proposed.
