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Published on: October 17, 2014
Identification of the cluster control region for the protocadherin-beta genes located beyond the protocadherin-gamma
Shinnichi Yokota1, Teruyoshi Hirayama, Keizo Hirano
1KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
Insights
Regulatory elements control clustered protocadherin (Pcdh) gene expression. Deleting specific elements impacts Pcdh-α and Pcdh-β isoform expression, revealing distinct regulatory mechanisms for neuronal diversity.
Area of Science:
- Neuroscience
- Genetics
- Molecular Biology
Background:
- Clustered protocadherins (Pcdhs) are transmembrane proteins crucial for neuronal diversity.
- Pcdh-α, -β, and -γ clusters exhibit stochastic and combinatorial expression in neurons.
- Understanding Pcdh gene regulation is key to deciphering neuronal identity.
Purpose of the Study:
- To investigate the in vivo function of a Pcdh-α regulatory element (HS5-1).
- To identify and characterize regulatory elements controlling Pcdh-β and Pcdh-γ expression.
- To elucidate the regulatory mechanisms governing clustered Pcdh gene expression.
Main Methods:
- Targeted deletion of DNase I hypersensitive (HS) site HS5-1.
- Identification and deletion of a Pcdh-β cluster control region (CCR) containing multiple HS sites.
- Analysis of Pcdh-α, -β, and -γ isoform expression levels in vivo.
Main Results:
- Deletion of HS5-1 specifically affected Pcdh-α isoform expression in vivo.
- A novel Pcdh-β CCR was identified downstream of the Pcdh-γ cluster.
- CCR deletion significantly decreased Pcdh-β expression and altered Pcdh-γ isoform levels, while not affecting Pcdh-α.
- The CCR demonstrated long-range cis-activation of upstream Pcdh-β genes.
Conclusions:
- Distinct regulatory elements control each clustered Pcdh gene cluster.
- The CCR is a specific regulatory unit for Pcdh-β expression.
- Complex chromatin architecture underlies the stochastic gene regulation of clustered Pcdhs, contributing to neuronal molecular diversity.
Abstract:
The clustered protocadherins (Pcdhs), Pcdh-α, -β, and -γ, are transmembrane proteins constituting a subgroup of the cadherin superfamily. Each Pcdh cluster is arranged in tandem on the same chromosome. Each of the three Pcdh clusters shows stochastic and combinatorial expression in individual neurons, thus generating a hugely diverse set of possible cell surface molecules. Therefore, the clustered Pcdhs are candidates for determining neuronal molecular diversity. Here, we showed that the targeted deletion of DNase I hypersensitive (HS) site HS5-1, previously identified as a Pcdh-α regulatory element in vitro, affects especially the expression of specific Pcdh-α isoforms in vivo. We also identified a Pcdh-β cluster control region (CCR) containing six HS sites (HS16, 17, 17', 18, 19, and 20) downstream of the Pcdh-γ cluster. This CCR comprehensively activates the expression of the Pcdh-β gene cluster in cis, and its deletion dramatically decreases their expression levels. Deleting the CCR nonuniformly down-regulates some Pcdh-γ isoforms and does not affect Pcdh-α expression. Thus, the CCR effect extends beyond the 320-kb region containing the Pcdh-γ cluster to activate the upstream Pcdh-β genes. Thus, we concluded that the CCR is a highly specific regulatory unit for Pcdh-β expression on the clustered Pcdh genomic locus. These findings suggest that each Pcdh cluster is controlled by distinct regulatory elements that activate their expression and that the stochastic gene regulation of the clustered Pcdhs is controlled by the complex chromatin architecture of the clustered Pcdh locus.
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