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Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12390-12399. doi: 10.1073/pnas.1900672116. Epub 2019 May 30.

Preformed chromatin topology assists transcriptional robustness of Shh during limb development.

Author information

1
Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
2
Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
3
Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
4
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
5
Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy.
6
Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy.
7
Berlin Institute of Health (BIH), Max Delbrück Center-Berlin, 13125 Berlin, Germany.
8
Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
9
Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
10
Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
11
Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; mundlos@molgen.mpg.de guillaume.andrey@unige.ch.

Abstract

Long-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time. However, in some cases, proximity coincides with gene activation, whereas, in others, preformed topologies already exist before activation. In this study, we investigate the preformed configuration underlying the regulation of the Shh gene by its unique limb enhancer, the ZRS, in vivo during mouse development. Abrogating the constitutive transcription covering the ZRS region led to a shift within the Shh-ZRS contacts and a moderate reduction in Shh transcription. Deletion of the CTCF binding sites around the ZRS resulted in the loss of the Shh-ZRS preformed interaction and a 50% decrease in Shh expression but no phenotype, suggesting an additional, CTCF-independent mechanism of promoter-enhancer communication. This residual activity, however, was diminished by combining the loss of CTCF binding with a hypomorphic ZRS allele, resulting in severe Shh loss of function and digit agenesis. Our results indicate that the preformed chromatin structure of the Shh locus is sustained by multiple components and acts to reinforce enhancer-promoter communication for robust transcription.

KEYWORDS:

3D genome; development; gene regulation; genetics; limb

PMID:
31147463
PMCID:
PMC6589666
[Available on 2019-11-30]
DOI:
10.1073/pnas.1900672116

Conflict of interest statement

The authors declare no conflict of interest.

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