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BioMed Research International
Volume 2015 (2015), Article ID 821596, 7 pages
http://dx.doi.org/10.1155/2015/821596
Research Article

Nucleosome Organization around Pseudogenes in the Human Genome

1The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
2School of Mathematics, Physics, and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou 014010, China

Received 9 September 2014; Accepted 17 December 2014

Academic Editor: Elena Papaleo

Copyright © 2015 Guoqing Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Pseudogene, disabled copy of functional gene, plays a subtle role in gene expression and genome evolution. The first step in deciphering RNA-level regulation of pseudogenes is to understand their transcriptional activity. So far, there has been no report on possible roles of nucleosome organization in pseudogene transcription. In this paper, we investigated the effect of nucleosome positioning on pseudogene transcription. For transcribed pseudogenes, the experimental nucleosome occupancy shows a prominent depletion at the regions both upstream of pseudogene start positions and downstream of pseudogene end positions. Intriguingly, the same depletion is also observed for nontranscribed pseudogenes, which is unexpected since nucleosome depletion in those regions is thought to be unnecessary in light of the nontranscriptional property of those pseudogenes. The sequence-dependent prediction of nucleosome occupancy shows a consistent pattern with the experimental data-based analysis. Our results indicate that nucleosome positioning may play important roles in both the transcription initiation and termination of pseudogenes.