Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology; Program in Cell and Developmental Dynamics; Program in Molecular Medicine
*Algorithms; Animals; Drosophila melanogaster; Gene Expression; Genomics; Humans; *Interspersed Repetitive Sequences; *Polymorphism, Genetic
Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Integrative Biology | Systems Biology
Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production.
TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git. Acids Research.
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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI of Published Version
Nucleic Acids Res. 2014 Jun;42(11):6826-38. doi: 10.1093/nar/gku323. Epub 2014 Apr 21. Link to article on publisher's site
Nucleic acids research
Zhuang J, Wang J, Theurkauf WE, Weng Z. (2014). TEMP: a computational method for analyzing transposable element polymorphism in populations. Program in Bioinformatics and Integrative Biology Publications. https://doi.org/10.1093/nar/gku323. Retrieved from https://escholarship.umassmed.edu/bioinformatics_pubs/55
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This work is licensed under a Creative Commons Attribution 3.0 License.