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    Selection pressure on human STR loci and its relevance in repeat expansion disease

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    Type
    Article
    Authors
    Shimada, Makoto K.
    Sanbonmatsu, Ryoko
    Yamaguchi-Kabata, Yumi
    Yamasaki, Chisato
    Suzuki, Yoshiyuki
    Chakraborty, Ranajit
    Gojobori, Takashi cc
    Imanishi, Tadashi
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Date
    2016-06-11
    Online Publication Date
    2016-06-11
    Print Publication Date
    2016-10
    Permanent link to this record
    http://hdl.handle.net/10754/621725
    
    Metadata
    Show full item record
    Abstract
    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases. © 2016, Springer-Verlag Berlin Heidelberg.
    Citation
    Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, et al. (2016) Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics 291: 1851–1869. Available: http://dx.doi.org/10.1007/s00438-016-1219-7.
    Sponsors
    We are grateful to Hidetoshi Inoko for support to use H-GOLD/GDBS data, Yasuyuki Fujii, Katsuhiko Murakami, Yoshiharu Sato and Jun-ichi Takeda for providing gene structure and annotation data, Ryuzo Matsumoto and Yosuke Hayakawa for useful suggestion on computer programming, and other former member of the H-Invitational 2 consortium, Genome Information Integration Project (GIIP), the Integrated Database and Systems Biology Team of BIRC, AIST for their helpful support. This research was financially supported by the Ministry of Economy, Trade and Industry of Japan (METI) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Grants-in-Aid for Scientific Research (C) to MKS (JSPS Grant Numbers 24510271 and 21510205), and the Saito Gratitude Foundation to MKS.
    Publisher
    Springer Nature
    Journal
    Molecular Genetics and Genomics
    DOI
    10.1007/s00438-016-1219-7
    PubMed ID
    27290643
    ae974a485f413a2113503eed53cd6c53
    10.1007/s00438-016-1219-7
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

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