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Evolutionary rate of human tissue-specific genes are related with transposable element insertions

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Abstract

The influence of transposable elements (TEs) on genome evolution has been widely studied. However, it remains unclear whether TE insertions also impact on evolutionary rate of human genes. In this study, we have compared the differences in TEs and evolutionary rates between human tissue-specific genes. Our results showed that various functional categories of human tissue-specific genes contained different TE numbers and divergent values of Ka/Ks, with human nucleic acid binding transcription factor activity genes having the fewest TE density and Ka/Ks value. Interestingly, we also found that human tissue-specific genes with TEs have also undergone faster evolution than those without TEs. Therefore, TEs have significant impact on the evolutionary rates of human tissue-specific genes. Furthermore, local genomic properties such as gene length, GC content and recombination rate may reflect a true transpositional bias for the particular TEs. Our results may provide important insights for further elucidating the evolution of human tissue-specific genes.

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Abbreviations

Ks :

Synonymous substitution rate

Ka :

Non-synonymous substitution rate

UTRs:

Untranslated regions

CDS:

Protein coding sequences

TEs:

Transposable elements

SINEs:

Short interspersed nuclear elements

LINEs:

Long interspersed nuclear elements

LTRs:

Long terminal repeat retrotransposons

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Acknowledgments

We are grateful to the two reviewers for their appropriate and constructive suggestions, and Alan K. Chang (Dalian University of Technology) for critically revising the manuscript,as well as to our colleagues for their suggestions and criticisms on the manuscript. This work has been jointly supported by grants from the National Natural Science Foundation of China (No. 30970348), the Project of New Century Excellent Talents in Universities (No. NCET-07-0405), and the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

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Correspondence to Fei Ma.

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Ping Jin and Sheng Qin are contributed equally to this work.

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10709_2013_9700_MOESM1_ESM.xls

Supplementary Table S1 The value of Ka, Ks and Ka/Ks, the numbers of different transposable elements in the intron and exon and the length of exon, intron and the whole gene of human tissue-specific genes (XLS 2530 kb)

10709_2013_9700_MOESM2_ESM.xls

Supplementary Table S2 The GO functional annotation of 691 human tissue-specific genes according to the molecular function (XLS 2880 kb)

10709_2013_9700_MOESM3_ESM.xls

Supplementary Table S3 The value of Ka, Ks and Ka/Ks and the TE density in exonic, intronic and the whole gene regions of the 691 human tissue-specific genes (XLS 106 kb)

Supplementary Table S4 The TE density in genes of different function categories (DOC 60 kb)

10709_2013_9700_MOESM5_ESM.doc

Supplementary Table S5 Correlation between various classes of TEs and gene length, GC content and recombination rate (DOC 50 kb)

10709_2013_9700_MOESM6_ESM.doc

Supplementary Table S6 Correlation between TE density and gene length (removing TE sequences), GC content (removing TE sequences) and recombination rate (DOC 38 kb)

10709_2013_9700_MOESM7_ESM.doc

Supplementary Table S7 Correlation between various classes of TEs and gene length (removing TE sequences), GC content (removing TE sequences) and recombination rate (DOC 51 kb)

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Jin, P., Qin, S., Chen, X. et al. Evolutionary rate of human tissue-specific genes are related with transposable element insertions. Genetica 140, 513–523 (2012). https://doi.org/10.1007/s10709-013-9700-2

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