Sequence configurations of the DM2 repeat in 24 primates species.

<p>Sequence configurations of the DM2 repeat in 24 primates species.</p

The Unstable CCTG Repeat Responsible for Myotonic Dystrophy Type 2 Originates from an <em>Alu</em>Sx Element Insertion into an Early Primate Genome

<div><p>Myotonic dystrophy type 2 (DM2) is a subtype of the myotonic dystrophies, caused by expansion of a tetranucleotide CCTG repeat in intron 1 of the zinc finger protein 9 (<em>ZNF9</em>) gene. The expansions are extremely unstable and variable, ranging from 75–11,000 CCTG repeats. This unprecedented repeat size and somatic heterogeneity make molecular diagnosis of DM2 difficult, and yield variable clinical phenotypes. To better understand the mutational origin and instability of the <em>ZNF9</em> CCTG repeat, we analyzed the repeat configuration and flanking regions in 26 primate species. The 3′-end of an <em>Alu</em>Sx element, flanked by target site duplications (5′-ACTRCCAR-3′or 5′-ACTRCCARTTA-3′), followed the CCTG repeat, suggesting that the repeat was originally derived from the <em>Alu</em> element insertion. In addition, our results revealed lineage-specific repetitive motifs: pyrimidine (CT)-rich repeat motifs in New World monkeys, dinucleotide (TG) repeat motifs in Old World monkeys and gibbons, and dinucleotide (TG) and tetranucleotide (TCTG and/or CCTG) repeat motifs in great apes and humans. Moreover, these di- and tetra-nucleotide repeat motifs arose from the poly (A) tail of the <em>Alu</em>Sx element, and evolved into unstable CCTG repeats during primate evolution. <em>Alu</em> elements are known to be the source of microsatellite repeats responsible for two other repeat expansion disorders: Friedreich ataxia and spinocerebellar ataxia type 10. Taken together, these findings raise questions as to the mechanism(s) by which <em>Alu</em>-mediated repeats developed into the large, extremely unstable expansions common to these three disorders.</p> </div

Nucleotide sequence comparison between human and prosimian intron 1 of the <i>ZNF9</i> gene.

<p>(A) Dot plot comparing the human <i>ZNF9</i> intron 1 (1359 bp, horizontal axis) with the corresponding region of the small-eared galago genome (1242 bp, vertical axis) by PipMaker. Blue, red, white boxes, and gray thick arrows denote dinucleotide (TG), tetranucleotide (TCTG and CCTG) repeat, poly (T) tract, and <i>Alu</i> element, respectively. Light blue dots indicate homologous region (56% identity) between the 131-bp region following human <i>Alu</i>Y and the 165-bp region following galago <i>Alu</i>Jo. Red dots indicates homologous region (67% identity) between human <i>Alu</i>Y and galago <i>Alu</i>Jo. (B) Sequence alignment between human <i>Alu</i>Y and small-eared galago <i>Alu</i>Jo. The aligned region corresponds to red dots shown in (A). <i>Alu</i> elements and flanking target site duplications are denoted as a gray thick arrow and white boxes, respectively. Dotted lines indicate sequence gaps.</p

Genomic structure of the human <i>ZNF9</i> gene and repetitive elements in and around the DM2 (TG)<i>_n</i>(TCTG)<i>_n</i>(CCTG)<i>_n</i> repeats.

<p>(A) Genomic alignment of the DM2 region from humans and other mammalian species. Filled thick arrows indicate DNA transposon (MER2) and short interspersed elements (<i>Alu</i>Sx and <i>Alu</i>Y). Blue, red, and purple boxes denote dinucleotide (TG), tetranucleotide (TCTG and CCTG) repeat regions, and the <i>ZNF9</i> exons, respectively. A yellow box highlights the regions corresponding to the human tetranucleotide repeat in other mammals. (B) Nucleotide sequence in and around the DM2 repeat of the human <i>ZNF9</i> gene. Each element is highlighted as follows: dinucleotide (TG) in blue; tetranucleotide (TCTG and CCTG) repeats in red; short interspersed elements (<i>Alu</i>Sx and <i>Alu</i>Y) in gray; and <i>ZNF9</i> exon 2 in purple. Black and white boxes flanking the <i>Alu</i>Sx and <i>Alu</i>Y elements, respectively, indicate target site duplications.</p

Supplementary Materials for Proteomic proling of archeological human bone from Proteomic profiling of archaeological human bone

Figure S1: STRING network of top 30 proteins. Figure S2: Enrichment GO term of the Biological Process. Figure S3: Enrichment GO term of the Cellular Component. Figure S4: Enrichment GO term of the Molecular Function. Figure S5: Relationship between age and the normalized emPAI value of proteins correlated with age. Table S1: Correlation between the unique peptides of neutrophil-derived proteins

Supplementary dataset from Proteomic profiling of archaeological human bone

Supplementary Dataset 1. emPAI value of detected proteins. Supplementary dataset 2. Normalized emPAI value of detected proteins