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Open Access Research article

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

Christoffer Nellåker1*, Fang Li1, Fredrik Uhrzander2, Joanna Tyrcha2 and Håkan Karlsson1

Author Affiliations

1 Department of Neuroscience, Karolinska Institutet, Retzius väg 8 B2:5, 17177 Stockholm, Sweden

2 Mathematical Statistics, Stockholms Universitet, Kräftriket Hus 6, 106 91 Stockholm, Sweden

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BMC Genomics 2009, 10:532  doi:10.1186/1471-2164-10-532

Published: 17 November 2009

Abstract

Background

Human 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.

Results

Applying 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.

Conclusion

Thus, 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.