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Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster.

Tan YP, Li S, Jiang XJ, Loh W, Foo YK, Loh CB, Xu Q, Yuen WH, Jones M, Fu J, Venkatesh B, Yu WP - Nucleic Acids Res. (2010)

Bottom Line: We provide evidence that protocadherin genes that do not contain an NRSE in their 5' intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes.We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs.Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

View Article: PubMed Central - PubMed

Affiliation: Gene Regulation Laboratory, National Neuroscience Institute, Singapore.

ABSTRACT
The clustered protocadherins are a subfamily of neuronal cell adhesion molecules that play an important role in development of the nervous systems in vertebrates. The clustered protocadherin genes exhibit complex expression patterns in the central nervous system. In this study, we have investigated the molecular mechanism underlying neuronal expression of protocadherin genes using the protocadherin gene cluster in fugu as a model. By in silico prediction, we identified multiple neuron-restrictive silencer elements (NRSEs) scattered in the fugu protocadherin cluster and demonstrated that these elements bind specifically to NRSF/REST in vitro and in vivo. By using a transgenic Xenopus approach, we show that these NRSEs regulate neuronal specificity of protocadherin promoters by suppressing their activity in non-neuronal tissues. We provide evidence that protocadherin genes that do not contain an NRSE in their 5' intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes. We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs. Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

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NRSEs in fugu protocadherin clusters. (A) Fugu protocadherin clusters. Colored vertical bars represent individual variable exons, whereas the black vertical bars at the 3′-end of each subcluster represent the constant exons. Red and blue ovals in the intergenic regions represent canonical and non-canonical NRSEs, respectively. The dotted line in the fugu Pcdh2 cluster indicates an undetermined sequence gap. Fr: Fugu rubripes. (B) WebLogo display of the consensus sequence of canonical (left panel) and non-canonical (right panel) NRSEs. Note: the non-canonical NRSE consensus is a combination of both fugu and zebrafish elements.
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Figure 1: NRSEs in fugu protocadherin clusters. (A) Fugu protocadherin clusters. Colored vertical bars represent individual variable exons, whereas the black vertical bars at the 3′-end of each subcluster represent the constant exons. Red and blue ovals in the intergenic regions represent canonical and non-canonical NRSEs, respectively. The dotted line in the fugu Pcdh2 cluster indicates an undetermined sequence gap. Fr: Fugu rubripes. (B) WebLogo display of the consensus sequence of canonical (left panel) and non-canonical (right panel) NRSEs. Note: the non-canonical NRSE consensus is a combination of both fugu and zebrafish elements.

Mentions: Fugu possesses two unlinked protocadherin clusters, Pcdh1 and Pcdh2, due to a whole genome duplication event in the fish lineage (23). While fugu Pcdh1 is a highly degenerate cluster that has lost the entire β and γ subclusters, and retained only two α and one δ subcluster genes, the fugu Pcdh2 consists of at least 74 genes belonging to the α, γ and δ subclusters (23,31). To identify potential regulatory elements, we searched for common sequence motifs in the intergenic regions of fugu Pcdh1 and Pcdh2 clusters using the motif-finding algorithm MEME (24). Our search identified a common sequence motif ‘TTCAGNACCANGGACAG’ present in the intergenic regions of 27 out of 74 genes in the fugu Pcdh2 cluster (Figure 1A, Supplementary Table S1). This motif does not overlap with the previously identified CGCT element in the mammalian (7,32) and elephant shark (31) protocadherin clusters. We searched for potential transcription factor binding sites in this motif using TESS (25) and discovered that this motif is highly similar to the NRSE, a 21-bp element that was initially identified in the regulatory region of SCG10 (superior cervical ganglion-10, also known as stathmin-2) and type II sodium channel genes (33,34), and was shown to mediate transcriptional repression of these neuronal genes in non-neuronal cells by binding to the transcriptional repressor, NRSF/REST (35,36). The consensus sequence of the fugu elements is highly similar to the consensus sequence of the NRSEs identified in the genomes of mammals (Figure 1B, left panel). No such NRSE-like motif was identified in fugu Pcdh1 cluster.Figure 1.


Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster.

Tan YP, Li S, Jiang XJ, Loh W, Foo YK, Loh CB, Xu Q, Yuen WH, Jones M, Fu J, Venkatesh B, Yu WP - Nucleic Acids Res. (2010)

NRSEs in fugu protocadherin clusters. (A) Fugu protocadherin clusters. Colored vertical bars represent individual variable exons, whereas the black vertical bars at the 3′-end of each subcluster represent the constant exons. Red and blue ovals in the intergenic regions represent canonical and non-canonical NRSEs, respectively. The dotted line in the fugu Pcdh2 cluster indicates an undetermined sequence gap. Fr: Fugu rubripes. (B) WebLogo display of the consensus sequence of canonical (left panel) and non-canonical (right panel) NRSEs. Note: the non-canonical NRSE consensus is a combination of both fugu and zebrafish elements.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 1: NRSEs in fugu protocadherin clusters. (A) Fugu protocadherin clusters. Colored vertical bars represent individual variable exons, whereas the black vertical bars at the 3′-end of each subcluster represent the constant exons. Red and blue ovals in the intergenic regions represent canonical and non-canonical NRSEs, respectively. The dotted line in the fugu Pcdh2 cluster indicates an undetermined sequence gap. Fr: Fugu rubripes. (B) WebLogo display of the consensus sequence of canonical (left panel) and non-canonical (right panel) NRSEs. Note: the non-canonical NRSE consensus is a combination of both fugu and zebrafish elements.
Mentions: Fugu possesses two unlinked protocadherin clusters, Pcdh1 and Pcdh2, due to a whole genome duplication event in the fish lineage (23). While fugu Pcdh1 is a highly degenerate cluster that has lost the entire β and γ subclusters, and retained only two α and one δ subcluster genes, the fugu Pcdh2 consists of at least 74 genes belonging to the α, γ and δ subclusters (23,31). To identify potential regulatory elements, we searched for common sequence motifs in the intergenic regions of fugu Pcdh1 and Pcdh2 clusters using the motif-finding algorithm MEME (24). Our search identified a common sequence motif ‘TTCAGNACCANGGACAG’ present in the intergenic regions of 27 out of 74 genes in the fugu Pcdh2 cluster (Figure 1A, Supplementary Table S1). This motif does not overlap with the previously identified CGCT element in the mammalian (7,32) and elephant shark (31) protocadherin clusters. We searched for potential transcription factor binding sites in this motif using TESS (25) and discovered that this motif is highly similar to the NRSE, a 21-bp element that was initially identified in the regulatory region of SCG10 (superior cervical ganglion-10, also known as stathmin-2) and type II sodium channel genes (33,34), and was shown to mediate transcriptional repression of these neuronal genes in non-neuronal cells by binding to the transcriptional repressor, NRSF/REST (35,36). The consensus sequence of the fugu elements is highly similar to the consensus sequence of the NRSEs identified in the genomes of mammals (Figure 1B, left panel). No such NRSE-like motif was identified in fugu Pcdh1 cluster.Figure 1.

Bottom Line: We provide evidence that protocadherin genes that do not contain an NRSE in their 5' intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes.We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs.Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

View Article: PubMed Central - PubMed

Affiliation: Gene Regulation Laboratory, National Neuroscience Institute, Singapore.

ABSTRACT
The clustered protocadherins are a subfamily of neuronal cell adhesion molecules that play an important role in development of the nervous systems in vertebrates. The clustered protocadherin genes exhibit complex expression patterns in the central nervous system. In this study, we have investigated the molecular mechanism underlying neuronal expression of protocadherin genes using the protocadherin gene cluster in fugu as a model. By in silico prediction, we identified multiple neuron-restrictive silencer elements (NRSEs) scattered in the fugu protocadherin cluster and demonstrated that these elements bind specifically to NRSF/REST in vitro and in vivo. By using a transgenic Xenopus approach, we show that these NRSEs regulate neuronal specificity of protocadherin promoters by suppressing their activity in non-neuronal tissues. We provide evidence that protocadherin genes that do not contain an NRSE in their 5' intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes. We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs. Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

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