Ancient traces of tailless retropseudogenes in therian genomes

Genome Biology and Evolution
Angela NollJürgen Schmitz

Abstract

Transposable elements, once described by Barbara McClintock as controlling genetic units, not only occupy the largest part of our genome but are also a prominent moving force of genomic plasticity and innovation. They usually replicate and reintegrate into genomes silently, sometimes causing malfunctions or misregulations, but occasionally millions of years later, a few may evolve into new functional units. Retrotransposons make their way into the genome following reverse transcription of RNA molecules and chromosomal insertion. In therian mammals, long interspersed elements 1 (LINE1s) self-propagate but also coretropose many RNAs, including mRNAs and small RNAs that usually exhibit an oligo(A) tail. The revitalization of specific LINE1 elements in the mammalian lineage about 150 Ma parallels the rise of many other nonautonomous mobilized genomic elements. We previously identified and described hundreds of tRNA-derived retropseudogenes missing characteristic oligo(A) tails consequently termed tailless retropseudogenes. Additional analyses now revealed hundreds of thousands of tailless retropseudogenes derived from nearly all types of RNAs. We extracted 2,402 perfect tailless sequences (with discernible flanking target site dupl...Continue Reading

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Citations

Apr 22, 2016·Scientific Reports·Zhenglin ZhuYong E Zhang
Oct 7, 2016·Nature Communications·Jürgen SchmitzWesley C Warren
Mar 12, 2016·PLoS Computational Biology·Andrej KuritzinGennady Churakov
Jun 1, 2018·Genome Biology and Evolution·Eri Nishiyama, Kazuhiko Ohshima
Jul 29, 2020·Genes·Kevin BatcherDanika Bannasch
Jun 21, 2021·Molecular Phylogenetics and Evolution·In-Su ChoiRobert K Jansen

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Software Mentioned

TSDfinder
RepeatMasker Library
BLASTN
R seqLogo
Python script
RepeatMasker
Python

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