ArticleNucleic acids research2014
CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation.
Article in Nucleic acids research, 2014. 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, 67 citations in OpenAlex.
- Direct analysis of transcription factor protected cfDNA in plasma by ChIP-seq: measurement of altered CTCF binding in cancer is a novel biomarker for liquid biopsy.Clinical epigenetics · 2026Article
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Gaining insights into Alzheimer's disease by predicting chromatin spatial organization.Bioinformatics advances · 2025Article
- Factors that determine cell type-specific CTCF binding in health and disease.Current opinion in genetics & development · 2024Review
- Genome access is transcription factor-specific and defined by nucleosome position.Molecular cell · 2024Article
- Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.Molecular neurobiology · 2024Article
- The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.Nature communications · 2024Article
- Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.Nature communications · 2024Article
- Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies.iScience · 2023Article
- Article
- Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions.iScience · 2023Article
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- CLIMB: High-dimensional association detection in large scale genomic data.Nature communications · 2022Article
- Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation.Protein & cell · 2022Article
- Article
- Enhancer architecture-dependent multilayered transcriptional regulation orchestrates RA signaling-induced early lineage differentiation of ESCs.Nucleic acids research · 2021Article
- Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.Nature communications · 2021Article
- Distinct properties and functions of CTCF revealed by a rapidly inducible degron system.Cell reports · 2021Article
- Understanding the role of Beclin1 in mouse embryonic stem cell differentiation through CRISPR-Cas9-mediated gene editing.Journal of biosciences · 2021Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18(th) position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site.
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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.