Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

BMC Medical Genomics

Dmitrij Frishman¹  Anja Mösch²  Kerstin Haase² 

[1] St Petersburg State Polytechnical University, St. Petersburg 195251, Russia;Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising 85354, Germany

关键词: Next-generation sequencing;    Cancer;    Gene expression;   

Others  :  1233845
DOI  :  10.1186/s12920-015-0146-5

 received in 2014-12-11, accepted in 2015-10-28,  发布年份 2015

【 摘 要 】

Background

Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which possess promoter activity and can therefore influence the expression of neighboring genes. HERV involvement in different types of cancer has already been thoroughly documented. However, so far there has been no systematic study of HERV expression patterns in a multitude of cell types in health and disease. In particular, the publication of the comprehensive ENCODE dataset has already facilitated many gene expression studies, but none so far focusing exclusively on HERVs.

Results

We present a comprehensive differential analysis of HERV expression based on ENCODE Tier 1 and Tier 2 RNA-seq data produced by Cold Spring Harbor Laboratories and the California Institute of Technology. This analysis was conducted for individual HERV loci and for entire HERV families in twelve different cell lines, of which six correspond to the normal condition and the other six represent cancer cell types. Although the principal component analysis revealed that the two groups of cells show distinguishable expression patterns, we were not able to link these differences to one or multiple particular HERV families. Two samples exhibit expression patterns, which are not similar to the corresponding cell lines of the other producing lab. Instead they show signs of cancer formation and expression of the pluripotency marker HERVH, despite being classified as a normal cell line and a differentiated cell, respectively.

Conclusions

Our study demonstrates that ENCODE data are generally comparable between the different contributing labs and that the analysis of HERV elements can provide novel insights into differentiation and disease state of a cell that are easily overlooked when focusing on protein-coding genes. Our findings hint at a change in HERV expression during cancerogenesis.

【 授权许可】

   
2015 Haase et al.

【 图 表 】

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