Ben Laufer and His Comments on “Gene Sequence but not Structure?”

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by Shea Robison (@EpigeneticsGuy)

Ben Laufer, an epigeneticist specializing in the effects of fetal alcohol exposure, recently left a comment to a recent post I wrote on the costs of excluding considerations of epigenetics when sequencing genomes for diagnostic and predictive purposes.

One main point of this original post is that not only is gene sequence important in gene expression, so is the physical three-dimensional structure of the genome. This structure is determined and manipulable through the interaction of the epigenome with its environment, which is the focus of study of epigenetics. As a result, while genome-focused approaches such as genome-wide association studies (GWASs) and genome-wide complex trait analyses (GCTAs) can reveal genetic sequences associated with certain outcomes, such processes are not able to account for the physical structures of genomes which also play a significant role in genetic expression, which means these more conventional methods of genetic analysis are missing a substantial part of the story. The take home point of the article is that the inclusion of epigenetic analyses with these more standard genomic analyses would go a long ways towards revealing the biological substrates of diseases and other issues.

In his comment, Ben affirms that when it comes to analyzing genes for diagnostic or predictive purposes, conventional practice is to “look at the genetic contribution and ignore the epigenome even though it can explain that missing heritability that is written off by many as ‘environment.'” Because of considerations like those just mentioned, Laufer writes, “research needs to focus on the complete picture, which is how genetic variation reacts with the epigenome to produce our phenotypes.”

In other words, genomics and epigenetics are not – or at least should not be – competing paradigms; rather “the disciplines are so intimately intertwined that they shouldn’t be considered separate disciplines,” and that instead of a competitor epigenetics is actually “the next evolutionary phase of Genetics.” These thoughts echo the sentiments of Dr. Randy Jirtle highlighted here and here about the unifying potential of epigenetics.

Laufer also comments about the nuts and bolts future of epigenetics,  Despite all the potential for significant discoveries yet to be made in epigenetics, Laufer writes that he fears the longstanding historical hostilities directed towards epigenetics – some of which are detailed here and here and here – still deter a lot of researchers who are on career paths in the sciences from engaging in epigenetics research. Ben sees a lack of public communication as instrumental in dispelling this lingering suspicion about epigenetics, and that epigenetics can only benefit from more public resources like this blog and and Dr. Jirtle’s outreach efforts in encouraging others to be engage in epigenetics research.

I want to thank Ben for taking the time to comment on this post and to offer the insights that he does as a person actively engaged in epigenetics research. If you would like to read more about Ben Laufer and his specific research interests and his views on epigenetics, check out his Internet hub here, or his Q&A on GermlineExposures.org, which also hosts a number of other Q&As with other experts in the field.

Do you think epigenetics is a competitor with genomics or the next evolutionary phase of genetics?

Do you think more researchers should be engaged in epigenetics, or not? I appreciate the example Ben provides as a lab researcher on a career path of his own who despite the hostility often directed towards epigenetics is still able to show that research in epigenetics need not be a controversy-filled dead end, but can actually be a respected career path (see this article and this article for a rundown of the market prospects of epigenetics-focused research). What else can be done to encourage young researchers to engage in epigenetics?

I am curious to hear what you think. Leave me a comment on this or any of the other posts on this blog and I will respond as soon as I can

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