Researchers identify DNA that may contribute to each person’s uniqueness

Building on a tool that they developed in yeast four years ago, researchers at the Johns Hopkins University School of Medicine scanned the human genome and discovered what they believe is the reason people have such a variety of physical traits and disease risks.

In a report published in the 25 June 2010 issue of Cell, the team identified a near complete catalog of the DNA segments that copy themselves, move around in, and insert themselves here and there in our genome. The insertion locations of these moveable segments – transposons – in each individual’s genome helps determine why some are short or tall, blond or brunette, and more likely or less likely to have cancer or heart disease. The researchers say that tracking the locations of transposons in people with specific diseases might lead to the discovery of new disease genes or mutations.

Using their specialised “chip” with DNA spots that contain all of the DNA sequences that appear in the genome, researchers applied human DNA from 15 unrelated people. The research team compared transposon sites first identified in the original published human “index” genome and found approximately 100 new transposon sites in each person screened.

“We were surprised by how many novel insertions we were able to find,” says Jef Boeke, PhD, ScD, an author on the article, a professor of molecular biology and genetics, and co-director of the High Throughput Biology Center of the Institute for Basic Biomedical Sciences at Johns Hopkins. “A single microarray experiment was able to reveal such a large number of new insertions that no one had ever reported before. The discovery taught us that these transposons are much more active than we had guessed.”

Each of the 15 different DNA samples used in the study was purified from blood cells before it was applied to a DNA chip. Transposons stick to spots on the DNA chip corresponding to where they’re normally found in the genome, letting the researchers locate new ones.

Boeke’s group first invented the transposon chip in 2006 for use in yeast. But, it was Kathleen Burns, MD, PhD, now an assistant professor of pathology at Johns Hopkins, who first got the chip to work with human DNA. “The human genome is much larger and more complex, and there are lots of look-a-like DNAs that are not actively moving but are similar to the transposons that we were interested in,” says Burns. The trick was to modify how they copied the DNA before it was applied over the chip. The team was able to copy DNA from the transposons of interest, which have just three different genetic code letters than other look-alike DNA segments.

“We’ve known that genomes aren’t static places, but we didn’t know how many transposons there are in each one of us; we didn’t know how often a child is born with a new one that isn’t found in either parent and we didn’t know if these DNAs were moving around in diseases like cancer,” says Burns. “Now we have a tool for answering these questions. This adds a whole dimension to how we look at our DNA.”

Scientists produce first-ever epigenetic landscape
map for tissue differentiation

Having charted the occurrence of a common chemical change that takes place while stem cells decide their fates and progress from precursor to progeny, a Johns Hopkins-led team of scientists has produced the first-ever epigenetic landscape map for tissue differentiation.

The details of this collaborative study between Johns Hopkins, Stanford and Harvard appear 15 August in the early online publication of Nature. The researchers, using bloodforming stem cells from mice, focused their investigation specifically on an epigenetic mark known as methylation. This change is found in one of the building blocks of DNA, is remembered by a cell when it divides, and often is associated with turning off genes.

Employing a customised genome-wide methylation-profiling method dubbed CHARM (comprehensive highthroughput arrays for relative methylation), the team analysed 4.6 million potentially methylated sites in a variety of blood cells from mice to see where DNA methylation changes occurred during the normal differentiation process. The team chose the blood cell system as its model because it’s well-understood in terms of cellular development.

They looked at eight types of cells in various stages of commitment, including very early blood stem cells that had yet to differentiate into red and white blood cells. They also looked at cells that are more committed to differentiation: the precursors of the two major types of white blood cells, lymphocytes and myeloid cells. Finally, they looked at older cells that were close to their ultimate fates to get more complete pictures of the precursor-progeny relationships – for example, at white blood cells that had gone fairly far in T-cell lymphocyte development. (Lymphoid and myeloid constitute the two major types of progenitor blood cells.)

“It wasn’t a complete tree, but it was large portions of the tree, and different branches,” says Andrew Feinberg, MD, MPH, King Fahd Professor of Molecular Medicine and director of the Center for Epigenetics at Hopkins’ Institute for Basic Biomedical Sciences.

“Genes themselves aren’t going to tell us what’s really responsible for the great diversity in cell types in a complex organism like ourselves,” Prof Feinberg says. “But I think epigenetics, and how it controls genes, can. That’s why we wanted to know what was happening generally to the levels of DNA methylation as cells differentiate.”

One of the surprising finds was how widely DNA methylation patterns vary in cells as they differentiate. “It wasn’t a boring linear process,” Prof Feinberg says. “Instead, we saw these waves of change during the development of these cell types.”

The data shows that when all is said and done, the lymphocytes had many more methylated genes than myeloid cells. However, on the way to becoming highly methylated, lymphocytes experience a huge wave of loss of DNA methylation early in development and then a regain of methylation. The myeloid cells, on the other hand, undergo a wave of increased methylation early in development and then erase that methylation later in development.

Rudimentary as it is, this first epigenetic landscape map has predictive power in the reverse direction, according to Prof Feinberg. The team could tell which types of stem cells the blood cells had come from, because epigenetically those blood cells had not fully let go of their past; they had residual marks that were characteristic of their lineage.

One apparent application of this work might be to employ these same techniques to assess how completely an induced pluripotent stem cell (iPSC) has been reprogrammed.

Because the data seem to indicate discreet stages of cell differentiation characterised by waves of changes in one direction and subsequent waves in another, cell types conceivably could be redefined according to epigenetic marks that will provide new insights into both normal development and disease processes.

“Leukemias and lymphomas likely involve disruptions of the epigenetic landscape,” Feinberg says. “As epigenetic maps such as this one begin to get fleshed out by us and others, they will guide our understanding of why those diseases behave the way they do, and pave the way for new therapies.”

● Reference: doi:10.1038/nature09367

● On the Web: Andrew Feinberg discusses the epigenetic map:

Researchers find five new genetic variations
linked to prostate cancer

A genome-wide study on Japanese subjects at the RIKEN Center for Genomic Medicine (CGM) and the University of Tokyo has identified 5 new genetic variations associated with prostate cancer and revealed differences and similarities between Europeans and Asians in susceptibility to the disease. Reported in Nature Genetics, the findings offer a first-ever glimpse of the genetic basis for prostate cancer susceptibility in a non-European population.

Despite having the lowest rates of prostate cancer in the world, Asian countries have experienced a rapid rise in incidence of the disease, which ranks as one of the world’s most prevalent forms of cancer. In Japan, Western lifestyles and an aging society have led to surging prostate cancer rates, contributing to growing public interest in understanding associated genetic factors. These findings highlight variation in susceptibility among ethnic populations. A better understanding of such variation promises more accurate risk assessment, improvements in screening protocols and more effective clinical treatment.

● Reference: doi:10.1038/ng.635

New method for identifying causes of x-linked genetic
disorders developed

An international consortium of scientists of Helmholtz Zentrum München and the University of Toronto has identified previously unknown potential disease genes in humans and mice. Genes on the X chromosome, which regulate embryonic development, are the focus of the current publication in the journal Genome Research. Men have only one X chromosome, and therefore mutations on this chromosome disproportionately affect males, frequently leading to serious diseases such as haemophilia, muscular dystrophy and mental retardation.

Scientists of Helmholtz Zentrum München led by Dr Heiko Lickert, principal investigator at the Institute of Stem Cell Research, in cooperation with the group led by Professor Janet Rossant at the Hospital for Sick Children in Toronto, investigated which X-linked genes are relevant to disease. They reported their findings in Genome Research.

In cooperation with the Gene Trap Consortium coordinated by Professor Wolfgang Wurst of the Institute of Developmental Genetics, 58 genes were tested. That corresponds to 10% of the syntenic (commonalities in the sequence of genes or gene fragments on different chromosome segments when comparing different species [here human and mouse]) genes on the X chromosome. 17 of these 58 genes are essential for embryonic development and for 9 of these genes, mouse models for human diseases were generated. These models will be studied in detail in follow-up studies in order to gain new insights about the causes of human diseases.

For the first time, the effect of the respective mutation on embryonic development could be shown without generating individual mouse models. Until now, mutation screens were essential to close such knowledge gaps, but such screens are associated with much effort and expense. “This study brings us much closer to our goal of understanding the genetic causes of all X-linked diseases,” Dr Lickert said.
● Citation: doi: 10.1101/gr.105106.110 

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