Diehard fans cinema aren’t satisfied by just watching a movie; they want to know everything about it, including how those amazing special effects are pulled off. In much the same way, scientists at the University of Bergen in Norway noticed extensive gene expression reprogramming in their experiments with pre-cancerous prostate cells and wanted to get a behind-the-scenes look at what’s going on.
In some of their previous work, author Xi-Song Ke and his team saw that gene expression in primary prostate cells undergoing an epithelial to mesenchymal transition (EMT), an early step towards malignancy, was massively changed. They figured that histone and DNA methylation was behind the alterations, but without a collector’s edition DVD with the “making of…” bonus features to refer to, they decided to profile their samples at multiple EMT stages for DNA methylation, H3K4me3 and H3K27me3 marks to find the answers.
The Scandinavian group ran their ChIP and MeDIP enriched samples for each mark on promoter and whole genome microarrays, then analyzed the results together to get an Avatar in 3D-like picture of the EMT re-organization, instead of the sketched out storyboard version that looking at one mark alone might give you. The approach uncovered some unique results…some of which challenge conventional epigenetic wisdom:
- Less DNA methylation was around in all three samples than H3K4me3 or H3K27me3, indicating that the histone modifications are doing most of the EMT work.
- H3K27me3 and DNA methylation are commonly thought of as repressive marks, but DNA methylation was shown to be just mildy repressive, and only when the active mark H3K4me3 wasn’t also present.
- Many genes had bivalent, or double, marks, in which cases H3K27me3 seemed to override H3K4, and H3K4me3 would overshadow DNA methylation.
- Transcription levels of genes with double marks are based on the relative balance of active and repressive marks, not just which ones are there.
- H3K4me3 and DNA methylation often modify the same gene, but not in the same region.
- Histone methylation increases while DNA methylation drops during EMT, and the histone changes correlate with gene expression even though DNA methylation doesn’t.
As the first work to detail the changing epigenetic modifications in cells as they reprogram their gene expression patterns, this paper provides new insights on the regulatory role of epigenetic marks.
Check out the full Director’s cut version of the paper at BMC Genomics, November 2010.