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Context-dependent enhancer function revealed by targeted inter-TAD relocation

Author

Listed:
  • Christopher Chase Bolt

    (School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)
    University of Geneva)

  • Lucille Lopez-Delisle

    (School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL))

  • Aurélie Hintermann

    (University of Geneva)

  • Bénédicte Mascrez

    (University of Geneva)

  • Antonella Rauseo

    (University of Geneva
    University of Geneva)

  • Guillaume Andrey

    (University of Geneva
    University of Geneva)

  • Denis Duboule

    (School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)
    University of Geneva
    Collège de France)

Abstract

The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.

Suggested Citation

  • Christopher Chase Bolt & Lucille Lopez-Delisle & Aurélie Hintermann & Bénédicte Mascrez & Antonella Rauseo & Guillaume Andrey & Denis Duboule, 2022. "Context-dependent enhancer function revealed by targeted inter-TAD relocation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31241-3
    DOI: 10.1038/s41467-022-31241-3
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    References listed on IDEAS

    as
    1. Christopher Chase Bolt & Lucille Lopez-Delisle & Bénédicte Mascrez & Denis Duboule, 2021. "Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Raquel Rouco & Olimpia Bompadre & Antonella Rauseo & Olivier Fazio & Rodrigue Peraldi & Fabrizio Thorel & Guillaume Andrey, 2021. "Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
    4. Marco Osterwalder & Iros Barozzi & Virginie Tissières & Yoko Fukuda-Yuzawa & Brandon J. Mannion & Sarah Y. Afzal & Elizabeth A. Lee & Yiwen Zhu & Ingrid Plajzer-Frick & Catherine S. Pickle & Momoe Kat, 2018. "Enhancer redundancy provides phenotypic robustness in mammalian development," Nature, Nature, vol. 554(7691), pages 239-243, February.
    5. Elphège P. Nora & Bryan R. Lajoie & Edda G. Schulz & Luca Giorgetti & Ikuhiro Okamoto & Nicolas Servant & Tristan Piolot & Nynke L. van Berkum & Johannes Meisig & John Sedat & Joost Gribnau & Emmanuel, 2012. "Spatial partitioning of the regulatory landscape of the X-inactivation centre," Nature, Nature, vol. 485(7398), pages 381-385, May.
    6. Ines Desanlis & Yacine Kherdjemil & Alexandre Mayran & Yasser Bouklouch & Claudia Gentile & Rushikesh Sheth & Rolf Zeller & Jacques Drouin & Marie Kmita, 2020. "HOX13-dependent chromatin accessibility underlies the transition towards the digit development program," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    7. Michael D. Shapiro & Melissa E. Marks & Catherine L. Peichel & Benjamin K. Blackman & Kirsten S. Nereng & Bjarni Jónsson & Dolph Schluter & David M. Kingsley, 2004. "Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks," Nature, Nature, vol. 428(6984), pages 717-723, April.
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