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PreprintCited by 77Genomics and Chromatin DynamicsChromatin Remodeling and CancerChromosomal and Genetic Variations

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

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Anania, Chiara, Acemel, Rafael D., Jedamzick, Johanna, Bolondi, Adriano, Cova, Giulia, Brieske, Norbert, Kühn, Ralf, Wittler, Lars +2 more·2021·Nature Genetics
DOI 10.1101/2021.04.14.439779PMC PMC9279147
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Abstract

Vertebrate genomes organize into topologically associating domains, delimited by boundaries that insulate regulatory elements from nontarget genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding site (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors such as CBS number and orientation. Combined deletions demonstrated that CBSs cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by nonconvergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.

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  • A single CTCF site might exert transcriptional insulation through additional mechanisms beyond simply driving physical insulation, possibly depending on site identity and flanking sequences.

    “This suggests that a single CTCF site might exert transcriptional insulation through additional mechanisms beyond simply driving physical insulation, possibly depending on site identity47 and flanking sequences16.”

    From Nonlinear control of transcription through enhancer–promoter interactions (2022) · cites this paper as [47]

    The Discussion (page unavailable) says boundary function depends on the characteristics of specific CTCF-binding sites and suggests that additional factors modulate their function. This supports the site-identity possibility attached to this citation. It does not establish that a single site provides transcriptional insulation through a mechanism beyond physical insulation; the Discussion instead reports that gene activation correlates with structural insulation strength. Flanking sequences are attached to a different citation in the citing sentence. (LLM, conf=0.83)

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Cited by

Sorted by citations

Authors
Anania, C., Acemel, R. D., Jedamzick, J., Bolondi, A., Cova, G., Brieske, N., Kühn, R., Wittler, L., Real, F. M., & Lupiáñez, D. G.
Affiliations
  • Max Delbrück Center (DE)
  • Max Planck Institute for Molecular Genetics (DE)
Corresponding author
Lupiáñez, Darío G.
ORCID
Venue
Nature Genetics
Publisher
openRxiv
Published
2021-04-14
Volume
54
Issue
7
Pages
1026-1036
ISSN
1061-4036 (ISSN-L)
DOI
10.1101/2021.04.14.439779
PMC
PMC9279147
OpenAlex
W4285013803
Cited by
77
References
1
Citations by year
2026: 7 · 2025: 13 · 2024: 22 · 2023: 23 · 2022: 8 · 2021: 4
FWCI
5.39
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
Funders
  • European Molecular Biology Organization (EMBO ALTF 537-2020)
  • Deutsche Forschungsgemeinschaft (EMBO ALTF 537-2020, GA2495/1-1)
  • Helmholtz Association (ERC-RA-0033)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
CTCF, topologically associating domains, CTCF binding sites, chromatin interactions, loop interference, gene expression regulation, developmental regulation, transgenic mouse model, chromatin organization
MeSH terms
CCCTC-Binding Factor, Animals, Binding Sites, Chromatin, Chromosomes, Genome, Mice, Genome-Wide Association Study

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