ArticleGenome biology2015
Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
- An updated catalog ofFrontiers in molecular neuroscience · 2023Pooled it
- A positive feedback loop between YTHDC1 and EP300 drives multiple myeloma tumorigenesis.Oncogene · 2026Article
- Transcriptome signatures for the identification of bevacizumab responders in ovarian cancer.Genome medicine · 2026Article
- ADNP regulates chromatin architecture and lineage fidelity during neural differentiation.PLoS genetics · 2026Article
- Navigating the landscape of direct cellular reprogramming with DiReG.NPJ systems biology and applications · 2026Article
- Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulation.Nature genetics · 2025Article
- Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells.Nature structural & molecular biology · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- CTCF-anchored chromatin loop dynamics during human meiosis.BMC biology · 2025Article
- Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.Nature communications · 2024Article
- Factors that determine cell type-specific CTCF binding in health and disease.Current opinion in genetics & development · 2024Review
- BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites.Genome biology · 2024Article
- Review
- Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.Nature communications · 2023Article
- Association of mutation and expression of the brother of the regulator of imprinted sites (BORIS) gene with breast cancer progression.Oncotarget · 2023Article
- Review
- NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A Therapeutic Vaccine Targeting Rat BORIS (CTCFL) for the Treatment of Rat Breast Cancer Tumors.International journal of molecular sciences · 2023Article
- Spermiogenesis alterations in the absence of CTCF revealed by single cell RNA sequencing.Frontiers in cell and developmental biology · 2023Article
- Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 6 institutions in 4 countries.
Funding
Abstract
backgroundCTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.
resultsHere we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells.
conclusionsWe discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells.
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