Posted for Brendan Maher
Yesterday, Nature published a map of human DNA methylation at singe base pair resolution, basically the precise location of millions of methyl groups hanging on the cytosine bases in the genome.
For the ‘omics’ lovers, this is the methylome, a subset of the epigenome which presumably also includes the extent of different modifications made to histone proteins and the attachment of other molecules known to influence gene expression.
No doubt journalists around the world had a difficult time wrapping their nut grafs around this one.
Defining what makes something “epigenetic” has been a prickly practice (one briefly outlined in a Nature news feature last year).
Purists say that it has to do with modifications to gene expression that do not involve mutation but are inherited at least from cell to cell during division,if not through sexual reproduction as well. The NIH, which funded the current work, defines it a bit more loosely, not tying the modifications down to inheritance.
Metaphors are helpful in explaining the importance of the epigenome, but they can be equally sticky.
The Guardian’s Ian Sample refers to the epigenome as an instruction manual. I hate to pick at other people’s metaphors, but instruction manuals are static things, like, um, the genome. The epigenome is more dynamic, differing from cell type to cell type. Referring to it as a pianist to the genome’s keyboard, choosing which chords to play is… well, a little better. But, how many pianists does one need to make a human?
In their press release on the study, the University of Western Australia got rather colourful calling the epigenome “the clothes that dress a genome, controlling the way genes are packaged and expressed without actually altering the underlying DNA code”.
Annabel McGilvray at ABC (the Australian one, not the American one) refers to the epigenome as “a map of chemical switches governing the operation of a human genome”. It’s an apt description although there are suspicions that some epigenetic effects are more like volume dials.
Also to her credit, she notes that cancer treatments based on our knowledge of epigenetics are in development (one, histone deacetylase inhibitor Vorinostat, has been approved for treating a type of lymphoma) if indeed their mode of action is a little unclear.
AFP carries on the switches theme but also describes a “subcellular landscape of chemical signposts”.
Andrea Anderson at GenomeWeb Daily News plays it straight for the science savvy set, avoiding the pitfalls of metaphor in this case, instead playing up the surprising extent of non-CG methylation.
Me? I’ve always liked the idea that if the genome is the book of life, the epigenome is how a specific cell type marks it up with highlighters. Most cells don’t need the whole genome, just the information that’s important for being, say, a heart cell or a brain cell. What’s your favourite metaphor?
Image: by hyperscholar via Flickr