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Genome-wide characterization of PRE-1 reveals a hidden evolutionary relationship between suidae and primates

Hao Yu, Qingyan Wu, Jing Zhang, Ying Zhang, Chao Lu, Yunyun Cheng, Zhihui Zhao, Andreas Windemuth, Di Liu, Linlin Hao
doi: https://doi.org/10.1101/025791
Hao Yu
1College of Animal Science, Jilin University, Changchun 130062, China
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Qingyan Wu
1College of Animal Science, Jilin University, Changchun 130062, China
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Jing Zhang
1College of Animal Science, Jilin University, Changchun 130062, China
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Ying Zhang
1College of Animal Science, Jilin University, Changchun 130062, China
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Chao Lu
1College of Animal Science, Jilin University, Changchun 130062, China
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Yunyun Cheng
1College of Animal Science, Jilin University, Changchun 130062, China
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Zhihui Zhao
1College of Animal Science, Jilin University, Changchun 130062, China
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Andreas Windemuth
3Abcam, Firefly BioWorks Inc, United States
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  • For correspondence: haolinlin@jlu.edu.cn liudi1963@163.com windemut@yahoo.com
Di Liu
2Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
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  • For correspondence: haolinlin@jlu.edu.cn liudi1963@163.com windemut@yahoo.com
Linlin Hao
1College of Animal Science, Jilin University, Changchun 130062, China
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  • For correspondence: haolinlin@jlu.edu.cn liudi1963@163.com windemut@yahoo.com
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Abstract

We identified and characterized a free PRE-1 element inserted into the promoter region of the porcine IGFBP7 gene whose integration mechanisms into the genome, including copy number, distribution preferences, capacity to exonize and phyloclustering pattern are similar to that of the primate Alu element. 98% of these PRE-1 elements also contain two conserved internal AluI restriction enzyme recognition sites, and the RNA structure of PRE1 can be folded into a two arms model like the Alu RNA structure. It is more surprising that the length of the PRE-1 fragments is nearly the same in 20 chromosomes and positively correlated to its fracture site frequency. All of these fracture sites are close to the mutation hot spots of PRE-1 families, and most of these hot spots are located in the non-complementary fragile regions of the PRE-1 RNA structure. Sequence homology analysis showed that the PRE-1 element seemed to share a common ancestor 7SL RNA with primates but was generated by different evolutionary model, which suggests that the suidae may be the closest relatives to primates in laurasiatheria.

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Posted August 31, 2015.
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Genome-wide characterization of PRE-1 reveals a hidden evolutionary relationship between suidae and primates
Hao Yu, Qingyan Wu, Jing Zhang, Ying Zhang, Chao Lu, Yunyun Cheng, Zhihui Zhao, Andreas Windemuth, Di Liu, Linlin Hao
bioRxiv 025791; doi: https://doi.org/10.1101/025791
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Genome-wide characterization of PRE-1 reveals a hidden evolutionary relationship between suidae and primates
Hao Yu, Qingyan Wu, Jing Zhang, Ying Zhang, Chao Lu, Yunyun Cheng, Zhihui Zhao, Andreas Windemuth, Di Liu, Linlin Hao
bioRxiv 025791; doi: https://doi.org/10.1101/025791

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