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Science China Life Sciences

, Volume 59, Issue 8, pp 839–849 | Cite as

Evolutionary direction of processed pseudogenes

  • Guoqing LiuEmail author
  • Xiangjun Cui
  • Hong Li
  • Lu Cai
Open Access
Research Paper

Abstract

While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection.

Keywords

GC content mutual information transcription factor binding motifs mutational bias recombination 

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© The Author(s) 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0), which permits use, duplication, adaptation, distribution, and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • Guoqing Liu
    • 1
    • 2
    • 4
    Email author
  • Xiangjun Cui
    • 1
    • 2
  • Hong Li
    • 3
  • Lu Cai
    • 1
    • 2
  1. 1.School of Life Science and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
  2. 2.Institute of Bioengineering and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
  3. 3.School of Physical Science and TechnologyInner Mongolia UniversityBaotouChina
  4. 4.Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of BioinformaticsUniversity of GeorgiaAthensUSA

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