Abstract
Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which contain the regulation part of the retrovirus. Remaining HERVs constitute 7% to 8% of the present day human genome, and most have been identified as solo LTRs. The HERV sequences have been associated with several molecular functions as well as certain diseases in human, but their roles in human diseases are yet to be established. We designed EnHERV to make accessible the identified endogenous retrovirus repetitive sequences from Repbase Update (a database of eukaryotic repetitive elements) that are present in the human genome. Defragmentation process was done to improve the RepeatMasker annotation output. The defragmented elements were used as core database in EnHERV. EnHERV is available at http://sysbio.chula.ac.th/enherv and can be searched using either gene lists of user interest or HERV characteristics. Besides the search function, EnHERV also provides an enrichment analysis function that allows users to perform enrichment analysis between selected HERV characteristics and user-input gene lists, especially genes with the expression profile of a certain disease. EnHERV will facilitate exploratory studies of specific HERV characteristics that control gene expression patterns related to various disease conditions. Here we analyzed 25 selected HERV groups/names from all four HERV superfamilies, using the sense and anti-sense directions of the HERV and gene expression profiles from 49 specific tissue and disease conditions. We found that intragenic HERVs were associated with down-regulated genes in most cancer conditions and in psoriatic skin tissues and associated with up-regulated genes in immune cells particularly from systemic lupus erythematosus (SLE) patients. EnHERV allowed the analysis of how different types of LTRs were differentially associated with specific gene expression profiles in particular disease conditions for further studies into their mechanisms and functions.
Highlights
The human genome carries virus genetic content and is part virus, in various eukaryote genomes [1]
Since long terminal repeats (LTRs) may drive the transcription of adjacent host genomic sequences [24], we developed EnHERV to analyze various human endogenous retroviruses (HERVs) patterns that may be associated with gene expression patterns in certain disease conditions
We investigated the association between HERVs and gene expression under various disease conditions, especially in systemic lupus erythematosus (SLE)
Summary
The human genome carries virus genetic content and is part virus, in various eukaryote genomes [1]. They have been known as interspersed repetitive sequences (IRSs) or transposable elements (TEs) because they can be copied or cut and placed in other regions of the human genome. The ability of TEs to move within genomes impact host genome evolution [2]. The majority of LTR retroelements are derived from human endogenous retroviruses (HERVs), and about 8% of the human genome is made of LTR retrotransposons. While a variety of LTR retrotransposons have been identified, only vertebrate-specific endogenous retroviruses (ERVs) are known to be active in mammalian genomes [5]. Some remaining HERV elements in a host genome are still active in their host genome
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