ArticleGenome biology2013
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 84 citations in OpenAlex.
- Machine learning reveals sequence and genomic context features underlyingbioRxiv : the preprint server for biology · 2026Article
- Evolution of CTCF binding sites in the human genome.Molecular biology and evolution · 2026Article
- YY1 in hematopoietic stem cells: epigenetic regulation, chromatin architecture, and aging.Current opinion in hematology · 2026Review
- Molecular Mimics: How Viral Genomes Dupe Their Host by Usurping CTCF to Establish Infection.Viruses · 2026Review
- EBNA leader protein orchestrates chromatin architecture remodeling during Epstein-Barr virus-induced B cell transformation.Nucleic acids research · 2025Article
- Transposable elements as genome regulators in normal and malignant haematopoiesis.Blood cancer journal · 2025Review
- Glucose-induced LINC01419 reprograms the glycolytic pathway by recruiting YBX1 to enhance PDK1 mRNA stability in hepatocellular carcinoma.Clinical and translational medicine · 2024Article
- Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.Genome biology and evolution · 2024Article
- YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle.Nature genetics · 2024Article
- Epigenetic Regulation of Mammalian Cardiomyocyte Development.Epigenomes · 2024Review
- BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.Briefings in bioinformatics · 2024Article
- The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity.Stem cell reports · 2023Article
- Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv : the preprint server for biology · 2023Article
- Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies.iScience · 2023Article
- Targeting Transcription Factor YY1 for Cancer Treatment: Current Strategies and Future Directions.Cancers · 2023Review
- Review
- Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen.Computational and structural biotechnology journal · 2023Article
- Characterizing collaborative transcription regulation with a graph-based deep learning approach.PLoS computational biology · 2022Article
- Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor.Nucleic acids research · 2022Article
- Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.BMC genomics · 2022Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundThe genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcription factor binding can contribute to the evolutionary stabilization of regulatory regions, we tested whether YY1 and CTCF co-binding could in part account for conservation of CTCF binding.
resultsCombined analysis of CTCF and YY1 binding in lymphoblastoid cell lines from seven primates, as well as in mouse and human livers, reveals extensive genome-wide co-localization specifically at evolutionarily stable CTCF-bound regions. CTCF-YY1 co-bound regions resemble regions bound by YY1 alone, as they enrich for active histone marks, RNA polymerase II and transcription factor binding. Although these highly conserved, transcriptionally active CTCF-YY1 co-bound regions are often promoter-proximal, gene-distal regions show similar molecular features.
conclusionsOur results reveal that these two ubiquitously expressed, multi-functional zinc-finger proteins collaborate in functionally active regions to stabilize one another's genome-wide binding across primate evolution.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.