Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues

Abstract

BackgroundHuman endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcription of genomic regions harboring such elements.ResultsApplying a recently developed technique for obtaining high resolution melting temperature data, we examined the frequency distributions of HERV-W gag element into 13 Tm categories in human tissues. Transcripts containing HERV-W gag sequences were expressed in non-random patterns with extensive variations in the expression between both tissues, including different brain regions, and individuals. Furthermore, the patterns of such transcripts varied more between individuals in brain regions than other tissues.ConclusionThus, regulated expression of non-coding regions of the human genome appears to include the HERV-W family of repetitive elements. Although it remains to be established whether such expression patterns represent leakage from transcription of functional regions or specific transcription, the current approach proves itself useful for studying detailed expression patterns of repetitive regions.

Comprehensive Analysis of Human Endogenous Retrovirus Group HERV-W Locus Transcription in Multiple Sclerosis Brain Lesions by High-Throughput Amplicon Sequencing

“…Nevertheless, we detected sometimes pronounced differences in HERV-W transcript levels between tissue samples, overall and locus specific, pointing to interindividual differences in HERV-W transcript levels. Such interindividual variation in HERV transcript levels was also observed in previous microarray-based experiments (27,50), and a strategy involving high-resolution melt-ing temperatures likewise suggested interindividual differences in HERV-W transcript levels (28). Interindividual variation in cellular-gene transcription levels is a well-known phenomenon caused by genetic variation (58)(59)(60).…”

“…This is supported by relative HERV-W transcript levels in samples MS4 and MS5, which were obtained from the same patient, yet the MS5 sample displayed slightly higher relative transcript levels. The above-mentioned high-resolution melting-temperature-based study also suggested differences in transcript levels between brain areas (28). However, specifically designed studies will be required to answer those questions.…”

“…Employing microarray strategies, HERV-W was found to be transcribed in testicular cancer and the placenta (25,26) and in different human brain regions (27). High-resolution meltingtemperature analysis indicated nonrandom patterns of HERV-W transcription and also provided evidence for variable transcript levels between individuals (28). A number of RT-PCR-based studies of HERV-W transcription were also performed in the MS context but have produced sometimes conflicting findings.…”

Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection

“…Although the involvement of syncytin-1 in the pathogenesis of any of these conditions remains to be established, detection of HERV transcripts in adult tissues is intriguing, as repetitive elements are generally considered to be transcriptionally silent. Contrary to this view, transcripts containing the HERV-W gag gene display low but diversified and tissue-specific expression (16). Moreover, experimental data from our laboratory suggest that a number of HERV-W loci, including the locus encoding syncytin-1, can be transactivated in a range of human cell lines of nonplacental origin in response to influenza A/WSN/33 virus infection (17).…”

“…RNA extraction and reverse transcription (RT) were carried out as previously described (17). Analyses of the melting temperatures (T m s) of HERV-W gag amplicons were performed as previously described (16,37). Data on frequency distributions into T m categories (mixing proportions) in different cultures were compared by chi-square tests (GraphPad Prism, version 3.02, software).…”