Selection pressure on human STR loci and its relevance in repeat expansion disease
Type
ArticleAuthors
Shimada, Makoto K.Sanbonmatsu, Ryoko
Yamaguchi-Kabata, Yumi
Yamasaki, Chisato
Suzuki, Yoshiyuki
Chakraborty, Ranajit
Gojobori, Takashi

Imanishi, Tadashi
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Computational Bioscience Research Center (CBRC)
Date
2016-06-11Online Publication Date
2016-06-11Print Publication Date
2016-10Permanent link to this record
http://hdl.handle.net/10754/621725
Metadata
Show full item recordAbstract
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 NatureJournal
Molecular Genetics and GenomicsPubMed ID
27290643ae974a485f413a2113503eed53cd6c53
10.1007/s00438-016-1219-7
Scopus Count
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