Genome-wide screen reveals new tricks of old genes

Process shows how mounds of data can be effectively managed

Johns Hopkins scientists have successfully used new techniques to search the yeast genome for genes that help keep copied chromosomes together, protecting the integrity of the organism’s genetic material during cell division.

By combining two genome-wide screens, the researchers were able to narrow down the dozens of genes identified by the first screen to just 17 that made both cut-offs — a number small enough to be cost- and time-efficient to consider in some detail. Their report appears in the April issue of Molecular Biology of the Cell.

“Data created from new genome-scanning techniques can be overwhelming. Reading all there is to know about 50 genes to figure out what new knowledge may be lurking in the haystack is very difficult,” says Forrest Spencer, Ph.D., associate professor in Hopkins’ McKusick-Nathans Institute of Genetic Medicine. “But by overlapping information from two screens, we were able to figure out what Mother Nature was trying to tell us that wasn’t too complicated for us to understand.”

While the researchers had hoped their screens would reveal new genes and their functions, they instead identified genes previously linked to two other aspects of shepherding genetic material during cell division. Fifteen of the highlighted genes were already known to help ensure the accuracy of copied DNA and two help move chromosomes to opposite ends of the dividing cell.

But the researchers’ results give these “old” genes new jobs, associating them with cohesion, the little-understood process of keeping a chromosome and its copy together until the cell is ready to split in two. If the “sister” chromosomes aren’t kept together, both copies could end up on one side of the dividing cell. Another problem is that the copies could undergo extra rearrangements, risking loss of important genes.

“If there’s no cohesion, the cell will die,” says Spencer. “However, if the process sometimes works and sometimes doesn’t, some cells survive but their genetic material gets scrambled.”

It’s that sometimes-yes-sometimes-no problem that Spencer and her team are trying to figure out, in part because it’s interesting biology, but also because genetic instability plays such a big role in the development of cancer in humans. No one knows exactly at what point errors enter the genetic material and aren’t fixed, but the intricacies of chromosomes’ manipulation during cell division seem a good place to start.

Postdoctoral fellow Cheryl Warren, Ph.D., started the search by screening 5,916 yeast genes — all at once — for ones needed for survival in the absence of a gene called ctf4, already known to be a critical component of cohesion. Twenty-six genes popped out of this screen, a type known as “synthetic lethal” since the yeast survive the loss of either one, but not both, genes.

However, the synthetic lethal effect of some, if not many, of the genes from this screen would be due to problems other than faulty cohesion, the researchers knew. “We had to do something else to get a manageable starting point,” says Warren.

So, using a technique she developed to identify whether a gene’s loss causes the genetic material to become scrambled, Warren tested those 26 genes to see which of them seemed most likely to contribute to genetic instability through their involvement in cohesion. In these experiments, markers were scattered throughout the yeast’s genetic material so she could easily tell if pieces of the genome moved or went missing when a gene was knocked out.

Only 17 of the 26 identified genes caused genetic instability when missing from the yeast genome. Fifteen of those genes are involved in double-checking whether newly formed strands of DNA matched the cell’s original genetic material and calling in “repairmen” as needed (a process called the “S-phase checkpoint”). The other two genes are part of the machinery previously known to help move the two sets of chromosomes to opposite sides of the dividing cell.

“By using both screens, we got a number that was small enough to follow-up on, and yet large enough to reveal a trend,” says Warren. “This is the first evidence that proteins involved in checking the DNA sequence are also involved in keeping sister chromosomes together, and it’s a great starting point for understanding more.”

The research was funded by the National Human Genome Research Institute, the National Institute for General Medical Sciences, and the National Heart, Lung, and Blood Institute, all components of the National Institutes of Health.

Authors on the report are Warren, Spencer, Mark Eckley, Marina Lee, Joseph Hanna, Adam Hughes, Brian Peyser and Chunfa Jie of the McKusick-Nathans Institute; and Rafael Irizarry of the Johns Hopkins Bloomberg School of Public Health.