Epigenome Project Finds Symphony in Cells

If all cells have the same genome, why do they look and act differently? The epigenome conducts each part in the symphony.

Nature‘s special issue this week is about epigenomics. The National Institutes of Health (NIH), now that the ENCODE project (a previous effort to understand how many genes are expressed) has reported its findings, has launched the REC project (Roadmap Epigenomics Consortium). This issue of Nature presents its first findings based on 111 reference epigenomes. REC seeks to understand what turns genes on and off: i.e., what regulates their behavior.

Every cell expresses about half of the 22,000 genes in the human genome. The others are controlled by “epigenetic factors” (beyond/above the gene) that can amplify them or repress them. These factors include methyl tags on the histone proteins around which DNA is wrapped, acetyl tags, promoters, enhancers, and other processes. PhysOrg put out a summary of the findings. Nature included ten articles and papers, including:

• An overview and forum where five scientists give different views on the meaning of epigenomics.
• An editorial about the future prospects for this “emerging science” of epigenetics for understanding inheritance and disease.
• An integrated analysis of the 111 human genomes.
• A paper about differences in gene expression across human tissues.
• A paper on research into how chromatin architecture is reorganized during stem cell differentiation.
• A paper about transcription factor binding dynamics during embryonic stem cell differentiation.
• A letter about using epigenetic footprinting to dissect now nerve networks form.
• A letter about how epigenetics defines the mutational landscape of cancer.
• A letter about epigenetics and Alzheimer’s disease.

Like ENCODE, this consortium owes little to evolutionary theory. Only 3 of the articles mention evolution, and those speak either of (1) “evolutionarily conserved” elements, or (2) hope that the work will shed light on evolution. Most of the articles seem impressed with the complexity of epigenomics. “The task at hand was, as researchers like to say, not trivial,” the Editors say. At this stage, researchers are still trying to find out what questions to ask.

The most entertaining entry in the issue is “Epigenome: The Symphony in Your Cells” by Kerri Smith. It includes a video of musicians playing excerpts of Beethoven’s 5th, explaining that all the musicians have the same score, but the conductor lets each player know when and what to play. That’s a pithy analogy as far as it goes, but the epigenome is made up of many parts that don’t seem to have an obvious leader, like the single conductor in the video. Is there a conductor? Much more work will be required to answer that question. Smith ends, “Taken together, the work demonstrates how a cell’s epigenome is complex and exquisitely arranged — just like a Beethoven symphony.”

For a lay introduction to epigenetics, see the video by Dr. Tom Woodward and Dr. James Gills, “The Mysterious Epigenome: What Lies Beyond DNA” on YouTube. Epigenetics is a scientific revolution in the making that may become as big as genetics itself. If you thought genetics pointed to intelligent design, wait till you see what appears to lie in store with epigenetics. It represents layers of informational complexity: codes regulating other codes in ways that will challenge the mutation-selection mechanism of Darwinism possibly to the breaking point. Already, it has been contributing to the demise of the “junk DNA” myth. Much of the genome that looked incomprehensible or unnecessary to Darwinians may prove to be the key to understanding inheritance, as researchers take the Darwin earplugs out and hear the symphony.