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Mapping the Shh long-range regulatory domain.

Eve Anderson1, Paul S Devenney1, Robert E Hill2

  • 1MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK.

Development (Cambridge, England)
|September 26, 2014
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Summary

Long-distance enhancers controlling gene expression, like for the Shh gene, operate within topological domains. These domains, identified using Hi-C, contain regulatory elements that influence gene activity and expression patterns.

Keywords:
EnhancersLong-range regulationMouseSleeping beauty transposonSonic hedgehog (Shh)Topological domains

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Area of Science:

  • Genomics
  • Developmental Biology
  • Molecular Genetics

Background:

  • Coordinated gene expression relies on DNA regulatory sequences and transcription factors to control spatiotemporal patterns.
  • The Sonic hedgehog (Shh) gene serves as a model for understanding how enhancers, located in large genomic regions, regulate gene expression.

Purpose of the Study:

  • To systematically map genomic features controlling Shh gene expression using a transposon-based reporter system.
  • To investigate the relationship between enhancer activity, topological domains, and gene regulation within the Shh locus.

Main Methods:

  • Utilized the Sleeping Beauty transposon system to disperse the lacZ reporter gene throughout the Shh genomic region.
  • Employed Hi-C technology to define topological associated domains (TADs) within the Shh locus.
  • Analyzed reporter gene expression to identify active regulatory elements and their spatial extent.

Main Results:

  • Enhancer activity was largely confined within a 900 kb topological associated domain (TAD) of the Shh locus.
  • Both proximal and distal Shh enhancers could activate reporter genes over long distances within the TAD, indicating promoter surveying capacity.
  • The housekeeping gene Rnf32, located within the Shh TAD, appeared to evade enhancer activity, suggesting a mechanism for regulating ubiquitous genes.
  • Shh TAD boundaries did not strictly limit enhancer activity, with expression decreasing stepwise near domain edges.

Conclusions:

  • Topological associated domains play a crucial role in organizing long-range enhancer activity and regulating gene expression patterns, such as for the Shh gene.
  • Enhancers within a TAD can interact with multiple regulatory elements and genes, including those located distally, within the confines of the domain.
  • The regulatory architecture of TADs may involve mechanisms that protect housekeeping genes from widespread enhancer effects.