When scientists mapped the DNA sequence of 3 billion bases in the human genome they uncovered the master blueprint of what makes a human being; now a team in the US has produced a high resolution map of the first complete human epigenome, the driver of gene expression that regulates how all the options offered in the genome are put together to make the unique person that grows in a particular environment. Understanding the epigenome is the key to understanding how genes affect health and disease under the influence of factors like lifestyle, diet and environment.

The work is described in a paper published in the 14 October online issue of Nature.

Senior author, Dr Joseph Ecker, professor and director of the Genomic Analysis Laboratory at the Salk Institute at La Jolla, California, and a member of the San Diego Epigenome Center told the press that:

“Being able to study the epigenome in its entirety will lead to a better understanding of how genome function is regulated in health and disease but also how gene expression is influenced by diet and the environment.”

Think of the epigenome as a template that is superimposed on the genome map. The template has variously placed holes, depending on what it is a template for. For example the template for making brain cells will have holes in a different place to the templates for making other types of cell. What shows through the holes are the genes that may be expressed, and what does not show through are genes that are not expressed.

Thus one can see how different templates superimposed on the same map allow different expressions of the map to emerge to make cells of different function, and also influence how well those cells work or not. The epigenome is the link between the genome (the potential human being) and the phenotype (the human being that actually develops in a given environment).

For the study, Ecker and colleagues compared the epigenomes of human embryonic stem cells and differentiated connective lung cells or fibroblasts. They found a tightly controlled but dynamic “landscape” (the template) of methyl-groups, a group of chemicals through which the epigenome acts on the genome to express and “blank off” certain genes.

The researchers discovered that stem cells appear to have a particular DNA methylation pattern, which may explain how they establish and maintain their pluripotent state, they said.

The growing field of epigenetics is changing how researchers investigate, and how doctors treat, disease. For instance some drugs designed to interact with the epigenome have already been approved for the treatment of lymphoma and lung cancer.

Ecker said that we don’t really know the full impact of such drugs until we understand how they affect the whole epigenome.

Dr Linda Birnbaum, director of the National Institute of Environmental Health Sciences, one of the NIH institutes that is funding the overall five-year Roadmap Epigenomics Program that this study is a part of, said:

“The science has matured to a point that we can now map the epigenome of a cell.”

“This paper documents the first complete mapping of the methylome, a subset of the entire epigenome, of 2 types of human cells – an embryonic stem cell and a human fibroblast line. This will help us better understand how a diseased cell differs from a normal cell, which will enhance our understanding of the pathways of various diseases,” explained Birnbaum.

So far we know that the epigenome interacts with the genome in two ways, but there could be more. One way targets the histone “spools” that DNA winds around and which controls access to DNA, and the other way is, as already touched on, is through methylation of the DNA, which modifies only the C of the four-letter DNA “alphabet” (A, G, C and T).

Ecker and his team started working on genomic methylation patterns some two years ago, after which co-first author Dr Ryan Lister, who is a postdoctoral researcher in Ecker’s lab, established a way to find out whether each C in the genome is methylated or not. Once he knew this, he was then able to layer an epigenomic map upon the exact genome it regulates.

Lister speeded up and perfected the method using Arabidopsis thaliana, a plant whose genome is 25 times smaller than the human one; he then applied the method to fibroblast cells and human embryonic stem cells.

“We wanted to know how the epigenome of a differentiated cell that’s programmed to perform a specific job differs from the epigenome of a pluripotent stem cell, that has the potential to turn into any other cell type,” said Lister.

They found more or less what they expected, but there was also a big surprise. As expected they found that most of the Cs followed by Gs in fibroblast cells carried a methyl-group, a pattern often referred to as CG-methylation. But then they discovered that in embryonic stem cells about a quarter of of the methylations did not follow the anticipated CG pattern.

“Non-CG methylation is not completely unheard of — people have seen it in dribs and drabs, even in stem cells,” said co-first author Dr Mattia Pelizzola, who is also a postdoctoral researcher in Ecker’s lab and who worked with Lister to laboriously extract and analyze the huge amount of epigenome data.

“The whole field had been focused on CG methylation, and non-CG methylation was often considered a technical artifact,” explained Pelizzola.

To verify their findings, the researchers then used a second emrbyonic stem cell line and fibroblast cells that had been programmed to become induced pluripotent stem (iPS) cells, targeting several regions in each.

“They both had the same high level of non-CG methylation, which was lost when we forced them to differentiate,” said Pelizzola.

The team now plans to look at how the human epigenome changes during normal development and various disease states.

“For the first time, we will be able to see the fine details of how DNA methylation changes in stem cells and other cells as they grow and develop into new cell types,” said Ecker.

“We believe this knowledge will be extremely valuable for understanding diseases such as cancer and possibly even mental disorders. Right now we just don’t know how the epigenome changes during the aging process or how the epigenome is impacted by our environment or diet,” he explained.

“Human DNA methylomes at base resolution show widespread epigenomic differences.”
Ryan Lister, Mattia Pelizzola, Robert H. Dowen, R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren & Joseph R. Ecker.
Nature Published online 14 October 2009.

Source: Salk Institute.

Written by: Catharine Paddock, PhD