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Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster.

Kaneko R, Abe M, Hirabayashi T, Uchimura A, Sakimura K, Yanagawa Y, Yagi T - Sci Rep (2014)

Bottom Line: Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive.Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation.These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.

View Article: PubMed Central - PubMed

Affiliation: Bioresource center, Gunma University Graduate School of Medicine.

ABSTRACT
Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.

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Expressional re-allocation in the duplicated Pcdh-α cluster, but no alteration in neighboring gene expression.(a) Genomic structure of the Pcdh-α cluster (upper; wild-type, lower; duplicated) and neighboring genes. (b) qRT-PCR analysis of neighboring genes in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt (n = 3) and dup (n = 3). (c) SNP analysis of transcripts for Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. (d) Expression levels of wild-type and 5′- and 3′-located duplicated isoforms of Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt/wt (n = 3), dup/dup (n = 3).
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f2: Expressional re-allocation in the duplicated Pcdh-α cluster, but no alteration in neighboring gene expression.(a) Genomic structure of the Pcdh-α cluster (upper; wild-type, lower; duplicated) and neighboring genes. (b) qRT-PCR analysis of neighboring genes in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt (n = 3) and dup (n = 3). (c) SNP analysis of transcripts for Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. (d) Expression levels of wild-type and 5′- and 3′-located duplicated isoforms of Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt/wt (n = 3), dup/dup (n = 3).

Mentions: Previous studies have indicated that tandem duplication may alter not only the expression of genes within the duplication boundaries but also of genes located in their genomic neighborhoods33. Prompted by these observations, we first quantified the expression levels of transcripts in the vicinity of the Pcdh-α cluster in the cerebellum of 4-week-old Pcdhαdup(2-c2)/dup(2-c2) mice. The analyzed non-Pcdh genes included Wdr55, Dnd1, Hars, Zmat2, and Vault, located about 130-kb ~ 170-kb upstream from the duplication's 5′ boundary and Slc25a2, Taf7, Diap1, and Hdac3, located about 480-kb ~ 780-kb downstream from the duplication's 3′ boundary (Fig. 2a). We found that the duplication did not alter the expression of the Pcdh-β, Pcdh-γ, or non-Pcdh genes, except for a small effect on Pcdh-β22 (Fig. 2b). These results indicated that the tandem duplication of exons Pcdh-α2 to Pcdh-αc2 did not exert long-range effects on the regulation of neighboring genes.


Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster.

Kaneko R, Abe M, Hirabayashi T, Uchimura A, Sakimura K, Yanagawa Y, Yagi T - Sci Rep (2014)

Expressional re-allocation in the duplicated Pcdh-α cluster, but no alteration in neighboring gene expression.(a) Genomic structure of the Pcdh-α cluster (upper; wild-type, lower; duplicated) and neighboring genes. (b) qRT-PCR analysis of neighboring genes in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt (n = 3) and dup (n = 3). (c) SNP analysis of transcripts for Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. (d) Expression levels of wild-type and 5′- and 3′-located duplicated isoforms of Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt/wt (n = 3), dup/dup (n = 3).
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Related In: Results  -  Collection

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Show All Figures
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f2: Expressional re-allocation in the duplicated Pcdh-α cluster, but no alteration in neighboring gene expression.(a) Genomic structure of the Pcdh-α cluster (upper; wild-type, lower; duplicated) and neighboring genes. (b) qRT-PCR analysis of neighboring genes in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt (n = 3) and dup (n = 3). (c) SNP analysis of transcripts for Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. (d) Expression levels of wild-type and 5′- and 3′-located duplicated isoforms of Pcdh-α1, Pcdh-α3, Pcdh-α5, Pcdh-α6, Pcdh-α7, Pcdh-α9, Pcdh-α10, Pcdh-α12, and Pcdh-αc2 in the cerebellum of 4-week-old wild-type and Pcdhαdup(2-c2)/dup(2-c2) mice. wt/wt (n = 3), dup/dup (n = 3).
Mentions: Previous studies have indicated that tandem duplication may alter not only the expression of genes within the duplication boundaries but also of genes located in their genomic neighborhoods33. Prompted by these observations, we first quantified the expression levels of transcripts in the vicinity of the Pcdh-α cluster in the cerebellum of 4-week-old Pcdhαdup(2-c2)/dup(2-c2) mice. The analyzed non-Pcdh genes included Wdr55, Dnd1, Hars, Zmat2, and Vault, located about 130-kb ~ 170-kb upstream from the duplication's 5′ boundary and Slc25a2, Taf7, Diap1, and Hdac3, located about 480-kb ~ 780-kb downstream from the duplication's 3′ boundary (Fig. 2a). We found that the duplication did not alter the expression of the Pcdh-β, Pcdh-γ, or non-Pcdh genes, except for a small effect on Pcdh-β22 (Fig. 2b). These results indicated that the tandem duplication of exons Pcdh-α2 to Pcdh-αc2 did not exert long-range effects on the regulation of neighboring genes.

Bottom Line: Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive.Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation.These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.

View Article: PubMed Central - PubMed

Affiliation: Bioresource center, Gunma University Graduate School of Medicine.

ABSTRACT
Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.

Show MeSH