Percepta:  Epigenetics has certainly been a hot topic.  We’re very glad to have a chance to speak with you and get your read on where the field is heading.  Now that the field has had a chance to develop, can you give our readers a brief summary of what is now encompassed in the field of epigenetics?

PJ:   Well that really depends who you ask. Many people incorporate different mechanisms and marks under the “epigenetics” umbrella category.  At EpiGenie, we generally cover anything related to DNA methylation, chromatin, and non-coding RNAs. Not all of these mechanisms may be “epigenetic” by strict definition since some like the “heritable” requirement some people use to define epigenetic processes, but we tend to take a looser classification. Some larger consortia, like NIH’s Roadmap Epigenomics buckets them in this manner as well.

Percepta:   As with any field it seems that there are certain “centers of excellence” that develop over time.  In your opinion, are there well known epigenetic centers that are recognized today?  If so what distinguishes them?

PJ:   Yes, but I think these centers are more broadly dispersed than other areas we’re used to because epigenetics is all over the map. Unlike genomic sequencing centers, stem cell centers of excellence, or comprehensive cancer centers, which all focus on a particular technology, researcher area, or disease; with epigenetics, its researchers, and the tools they deploy are very diverse.

I’d say many of the Reference Epigenome Mapping and Data centers in the Roadmap Epigenomics program operate as Centers of Excellence, not just because of that name, but more why they were selected to champion different roles in the program; often these were the same labs and PIs that lobbied for such a program to begin with. They were the folks pushing the pace for the last decade in their own work.

But, there are so many labs that could be considered center of excellence. How about the team up at USC? Dr. Laird runs the Epigenome Center and Dr. Jones ran the Cancer Center for some time, and now has teamed up with Dr. Baylin in Stand Up to Cancer Dream Team for Epigenetics which has an entirely different funding angle and approach. I also think Johns Hopkins is one big center of excellence for epigenetics with the whole team over there. Go listen to one of Dr. Feinberg’s talks and you’ll see why.

Percepta: What would you say are some of the more vexing challenges in the field of epigenetics these days?

PJ:  There’s quite a long list of challenges, so I’ll just name a few. Unlike a relatively stable genome, epigenomic mechanisms can be very dynamic, they can very from cell to cell, and tremendously between individuals. Stabilizing a “snapshot” of an epigenome in a given state so that it can be read by a technology of choice, ideally at a single cell level is impossible today. It’s pretty easy to group those challenges into one sentence, but it will probably take years before that’s all possible.

Also, capturing a snapshot is nice, but one of the more intriguing aspects of epigenetics processes is that they can fluctuate in response to stimuli and development states. I think researchers would love to visualize these in real time and tie them to cellular phenotypes, but that is very complicated today.

Percepta: From your point of view, what are some of the more exciting and promising epigenetic research areas that have a chance to make epigenetics more of a household term?

PJ: I think the crossover into areas likes nutrition and environmental exposures. These are fascinating areas where epigenetics could play a key role in the molecular interface between our health and those leafy greens we’re supposed to be eating. Every day we hear about studies that link this habit to that outcome, many of which contradict each other. There’s so much to learn about how our diet and other habits can impact our bodies and progeny. Epigenetic mechanisms are starting to emerge as a promising vehicle to better understand this relationship.

Percepta:  Pete you have built a really well respected and valuable resource with EpiGenie (epigenie.com)   Tell us a bit about what you have been working on at Epigenie.

PJ:  The last six years, we’ve been working hard to make it easier for researchers in the epigenetics community to stay abreast of what’s going on, while simultaneously celebrating the teams that have been working really hard to produce interesting data. Researchers are good at their job, but they’re generally lousy at self-promotion, so we see ourselves as part news site and part PR vehicle for the hard working labs out there, with a sprinkle of industry content marketing to keep the lights on and fund surf trips.