title: Evolutionary direction of processed pseudogenes.
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.
authors.affiliation: School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China. gqliu1010@163.com.|Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China. gqliu1010@163.com.|Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA. gqliu1010@163.com.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Liu
authors.affiliation: School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.|Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Cui
authors.affiliation: School of Physical Science and Technology, Inner Mongolia University, Baotou, 010021, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.|Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Cai
mesh_terms: D000465:Algorithms; D001482:Base Composition / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D011544:Pseudogenes / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D009707:Nucleosomes; D014157:Transcription Factors
keywords: GC content; mutational bias; mutual information; recombination; transcription factor binding motifs