DNA Ethylation Changes and Evolution of RNA-Based Duplication in Sus Scrofa: Based on a Two-Step Strategy

Abstract

Aim: This study aims to couple DNA methylation changes and evolution of retrogenes. Materials & methods: A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. Results: A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits. Retrogenes were consistently hypermethylated. Hypomethylation of parental genes presented more susceptibility to retroposition. Promoter DNA methylation of retrogenes was negatively correlated with evolutionary time and played important roles in regulating retrogene tissue-specific expression pattern. Conclusion: A two-step procedure is effective and necessary for identifying retrogenes. DNA methylation drives origination, survival, evolution and expression of retrogenes.

Keywords::

• DNA methylation
• evolution
• new gene
• retrogenes
• two-step strategy

Financial & competing interests disclosure

This work was supported by a grant from National Natural Science Foundation of China (NSFC, No. 31601859 and 31472076), the Science Fund for Distinguished Young Scholars of Hubei Province of China (2014CFA024), the Research Project of Chinese Ministry of Education (113048A) and the National Basic Research Priorities Program of China (973 Program, 2013CB835205). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/full/10.2217/epi-2017-0071