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

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...

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Autores principales: Haase, Kerstin, Mösch, Anja, Frishman, Dmitrij
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632268/
https://www.ncbi.nlm.nih.gov/pubmed/26530187
http://dx.doi.org/10.1186/s12920-015-0146-5
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author Haase, Kerstin
Mösch, Anja
Frishman, Dmitrij
author_facet Haase, Kerstin
Mösch, Anja
Frishman, Dmitrij
author_sort Haase, Kerstin
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12920-015-0146-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-46322682015-11-04 Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data Haase, Kerstin Mösch, Anja Frishman, Dmitrij BMC Med Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12920-015-0146-5) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-03 /pmc/articles/PMC4632268/ /pubmed/26530187 http://dx.doi.org/10.1186/s12920-015-0146-5 Text en © Haase et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Haase, Kerstin
Mösch, Anja
Frishman, Dmitrij
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title_full Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title_fullStr Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title_full_unstemmed Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title_short Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data
title_sort differential expression analysis of human endogenous retroviruses based on encode rna-seq data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632268/
https://www.ncbi.nlm.nih.gov/pubmed/26530187
http://dx.doi.org/10.1186/s12920-015-0146-5
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