ArticleNucleic acids research2024
The characteristics of CTCF binding sequences contribute to enhancer blocking activity.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Single-allele nanoscale mapping of regulatory variants.Nature genetics · 2026Article
- Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation.Nature communications · 2026Article
- Cohesin bridging as a physical principle of enhancer-promoter communication.bioRxiv : the preprint server for biology · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activity.PloS one · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
- Active regulatory elements recruit cohesin to establish cell specific chromatin domains.Scientific reports · 2025Article
- Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2.PLoS computational biology · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
While the elements encoding enhancers and promoters have been relatively well studied, the full spectrum of insulator elements which bind the CCCTC binding factor (CTCF), is relatively poorly characterized. This is partly due to the genomic context of CTCF sites greatly influencing their roles and activity. Here we have developed an experimental system to determine the ability of minimal, consistently sized, individual CTCF elements to interpose between enhancers and promoters and thereby reduce gene expression during differentiation. Importantly, each element is tested in the identical location thereby minimising the effect of genomic context. We found no correlation between the ability of CTCF elements to block enhancer-promoter activity with the degree of evolutionary conservation; their resemblance to the consensus core sequences; or the number of CTCF core motifs harboured in the element. Nevertheless, we have shown that the strongest enhancer-promoter blockers include a previously described bound element lying upstream of the CTCF core motif. In addition, we found other uncharacterised DNaseI footprints located close to the core motif that may affect function. We have developed an assay of CTCF sequences which will enable researchers to sub-classify individual CTCF elements in a uniform and unbiased way.
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