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Conservation of intronic minisatellite polymorphisms in the SCK1/SHC2 gene of Hominidae


The neuronally expressed Shc adaptor homolog SCK1/SHC2 gene contains an unusually high number of minisatellites. In humans, twelve different minisatellite sequences are located in introns of SCK1/SHC2 and ten of them are highly polymorphic. Here we used primers developed for humans to screen ten intronic loci of SCK1/SHC2 in chimpanzee and gorilla, and undertook a comprehensive analysis of the genomic sequence to address the evolutionary events driving these variable repeats. All ten loci amplified in chimpanzee and gorilla contained hypervariable and low-variability minisatellites. The human polymorphic locus TR1 was monomorphic in chimpanzee and gorilla, but we detected polymorphic alleles in these apes for the human monomorphic TR7 locus. When we examined the repeat size among these hominoids, there was no consistent variation by length from humans to great apes. In spite of the inconsistent evolutionary dynamics in repeat length variation, exon 16 was highly conserved between humans and great apes. These results suggest that non-coding intronic minisatellites do not show a consistent evolutionary paradigm but evolved with different patterns among each minisatellite locus. These findings provide important insight for minisatellite conservation during hominoid evolution.

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This work was supported by the Dong-A University research fund.

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Correspondence to Sun-Hee Leem.

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Se-Lyun Yoon and Yunhee Jeong contributed equally to this study.

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Suppl. Figure S1. Association of minisatellites and other repeats in the human SCK1/SHC2 gene. A schematic diagram of the sequence spanning the SCK1/SHC2 gene is shown. (a) The approximate positions of minisatellites are indicated by asterisks. On top, a blown up portion of the insert shows the relative positions within introns of the twelve minisatellites. Ten minisatellites (TR1, 2, 3, 4, 7, 8, 9, 10, 11 and 12) analyzed for non-human hominoids were presented in black boxes on top. (b) The positions of transposable elements (MLT1C, MER20B) were predicted by RNAfold Webserver. Suppl. Figure S2. Graphical representations of individual allele size distributions for species and loci. The distributions are presented for human (white), chimpanzee (black) and gorilla (gray). Suppl. Figure S3. Hairpin structure of transposable elements. The secondary structures of two palindromic consensus sequences (MLT1C, MER20B) were predicted by the RNAfold Webserver. Consensus sequences containing palindromic sequences were referred from the Repbase browser of the Genetic Information Research Institute database. There size and minimum free energy are presented as MLT1C: 467 bp, -138.30 kcal/mol, MER20B: 783 bp, -256.20 kcal/mol, respectively. (PDF 172 kb)

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Yoon, SL., Jeong, Y., Kim, HS. et al. Conservation of intronic minisatellite polymorphisms in the SCK1/SHC2 gene of Hominidae. Genes Genom 36, 375–385 (2014).

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  • SCK1/SHC2
  • Great apes
  • Minisatellites
  • Molecular evolution