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A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

Author

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  • A. Rasim Barutcu

    (Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard)

  • Philipp G. Maass

    (Harvard University)

  • Jordan P. Lewandowski

    (Harvard University
    Beth Israel Deaconess Medical Center)

  • Catherine L. Weiner

    (Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard
    Beth Israel Deaconess Medical Center
    Harvard University)

  • John L. Rinn

    (Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard
    Beth Israel Deaconess Medical Center
    Harvard University)

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.

Suggested Citation

  • A. Rasim Barutcu & Philipp G. Maass & Jordan P. Lewandowski & Catherine L. Weiner & John L. Rinn, 2018. "A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03614-0
    DOI: 10.1038/s41467-018-03614-0
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    Cited by:

    1. Evelyn Kabirova & Anastasiya Ryzhkova & Varvara Lukyanchikova & Anna Khabarova & Alexey Korablev & Tatyana Shnaider & Miroslav Nuriddinov & Polina Belokopytova & Alexander Smirnov & Nikita V. Khotskin, 2024. "TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. David E. Torres & H. Martin Kramer & Vittorio Tracanna & Gabriel L. Fiorin & David E. Cook & Michael F. Seidl & Bart P. H. J. Thomma, 2024. "Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Xiao Ge & Haiyan Huang & Keqi Han & Wangjie Xu & Zhaoxia Wang & Qiang Wu, 2023. "Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Christian Much & Erika L. Lasda & Isabela T. Pereira & Tenaya K. Vallery & Daniel Ramirez & Jordan P. Lewandowski & Robin D. Dowell & Michael J. Smallegan & John L. Rinn, 2024. "The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Roger Mulet-Lazaro & Stanley Herk & Margit Nuetzel & Aniko Sijs-Szabo & Noelia Díaz & Katherine Kelly & Claudia Erpelinck-Verschueren & Lucia Schwarzfischer-Pfeilschifter & Hanna Stanewsky & Ute Acker, 2024. "Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

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