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| Status |
Public on May 03, 2016 |
| Title |
Shh and ZRS enhancer co-localization is specific to the zone of polarizing activity |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Limb-specific expression of Shh is regulated by the long-range (~one megabasepair distant) ZRS enhancer. In the mouse, murine limb bud restricted spatiotemporal expression of Shh occurs from ~E10 until E11.5 at the distal posterior margin is essential for the correct formation of the autopod. Here, we have analyzed the higher-order chromatin conformation of Shh in expressing and non-expressing tissues, both by fluorescence in situ hybridization (FISH) and by chromosome conformation capture (5C). Conventional and super-resolution light microscopy identified significantly elevated frequences of Shh/ZRS co-localization only in the Shh expressing regions of the limb bud consistent with the formation of an enhancer-promoter loop. However, Shh-ZRS spatial distances were consistently shorter than intervening distances to a neural enhancer in all tissues and developmental stages analyzed – regardless of Shh expression. 5C also identified a topologically associating domain (TAD) over the Shh-ZRS genomic region and enriched interactions between Shh and ZRS, but in the head, body and limb buds of E11.5 embryos, so also not linked to Shh expression. We show that gene-enhancer (Shh/ZRS) co-localization correlates with the spatiotemporal domain of limb bud-specific Shh expression, but that close Shh/ZRS proximity in the nucleus occurs regardless of whether the gene or enhancer is active. We suggest that this constrained chromatin configuration optimises the opportunity for the active enhancer to locate and instigate Shh expression.
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| Overall design |
Here, we have analyzed the higher-order chromatin conformation of Shh in expressing and non-expressing tissues by chromosome conformation capture (5C).
5C oligonucleotides were designed around HindIII restriction sites following an alternative scheme
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| Contributor(s) |
Williamson I, Lettice LA, Hill RE, Bickmore WA |
| Citation(s) |
27402708 |
| |
| Submission date |
Apr 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Iain Williamson |
| E-mail(s) |
Iain.Williamson@igmm.ed.ac.uk
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| Organization name |
IGMM MRC Human Genetics Unit
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| Department |
Chromosomes and Gene Expression
|
| Lab |
Wendy Bickmore
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA317475 |
| SRA |
SRP072886 |
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