ArticleNature communications2018
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed, 131 citations in OpenAlex.
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- The Transcription Factor FgSge1 Harnesses the SAGA Complex to Activate Mycotoxin Biosynthesis and Fungal Virulence.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- Targeting long non-coding RNAMolecular therapy. Nucleic acids · 2025Article
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- Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity.Nature communications · 2025Article
- The 3D genome of plasma cells in multiple myeloma.Scientific reports · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Deletion of an evolutionarily conserved TAD boundary impacts spermatogenesis in mice†.Biology of reproduction · 2025Article
- Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization.Nucleic acids research · 2025Article
- X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes.Nature communications · 2024Article
- Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome.Genomics, proteomics & bioinformatics · 2024Article
- The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation.Nature communications · 2024Article
- Biochemical properties of chromatin domains define genome compartmentalization.Nucleic acids research · 2024Article
- Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia.Nature communications · 2024Article
- TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.Nature communications · 2024Article
- LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells.The EMBO journal · 2024Article
- Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.Nature communications · 2024Article
- Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation.Nature communications · 2023Article
- Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here we test the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~ 15 CTCF binding sites and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-specific or allele-specific manner. In contrast, Firre's deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation.
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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.