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Hunting for hot spots for chromosome reshuffling

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Researchers map where in the genome chromosomes rejoin after breaking; could help guide understanding of cancer genomics and efforts to develop gene therapies

September 29, 2011

Boston, Mass. – Researchers at Children’s Hospital Boston and the Immune Disease Institute (IDI) have created a method for mapping “hot spots” in the genome where chromosomes are most likely to break and recombine, knowledge that help define the rules that govern when and where breaks occur. An understanding of these rules could change the way scientists think about aspects of cancer genomics and also help guide ongoing efforts to develop gene therapy-based treatments for a variety of conditions.

The research team, led by Frederick Alt, PhD, director of the IDI and the Program in Cellular and Molecular Medicine at Children’s Hospital Boston, reported their results in the September 30 issue of Cell.

In many cancers, whole chromosomes get rearranged or recombined, physically breaking and swapping sections with other chromosomes. These rearrangements, called translocations, connect portions of two genes together to create new “fusion” genes that sometimes combine the functions of the original pair to create a cancer gene.

“People have been characterizing translocations for the last 50 years or so,” said Alt, who is also a Howard Hughes Medical Institute investigator and the Charles A. Janeway Professor of Pediatrics at Harvard Medical School, “but we haven’t understood the mechanisms that form them. We know what happened, but not how it happened.

“This study,” he continued, “helps define what those mechanisms are.”

To better understand the rules that govern where in the genome breaks occur and where a broken piece of a chromosome will land, Alt and his colleagues developed a method for mapping what they call the “translocatome” – the total genome-wide complement of rearrangements for a particular chromosome break. The method, called high-throughput genome-wide translocation sequencing (HTGTS), is based on the action of DNA-cutting enzymes such as I-SceI, a general type of enzyme that is also under scrutiny as a possible gene therapy tool and which Alt’s team used in the current study.

The team found that the broken chromosome segments tend to fuse near the beginnings of genes, at locations called transcription start sites. “The frequency at which translocations occur at transcription start sites is extremely high,” Alt explained, “implying that something about the transcription process itself might encourage chromosome breaks.”

In addition, they have also found that broken chromosomes often rearrange within themselves, as opposed to sharing pieces across different chromosomes. “We’re still in the process of defining what all the translocation rules are,” Alt noted, “but we think that because chromosomes tend to fold into balls, broken ends within a given chromosome tend to be physically closer to each other than to breaks on other chromosomes.”

This greater understanding of where and the rules by which translocations occur could lead to a new way of thinking about how particular genes and translocations contribute to cancer. For instance, HTGTS could help scientists figure out which  oncogenes might contribute to different tumors by showing which have a high potential for containing translocation sites in tumor progenitors.

The method could help also cancer genome researchers determine which translocations in a particular tumor actually play a role in the tumor’s growth and survival and which are, in essence, innocent bystanders.

“Childhood cancers, from leukemias and lymphomas to neuronal tumors, all have an inherent genomic instability that manifests itself in translocations,” said Alt. “But while translocations come up very frequently across the cancer genome, it’s the ones that the cells select for that are important. Our work could help concentrate efforts to understand cancer translocations on those that are related to tumor initiation and which could have some therapeutic value.”

Alt’s team also found that the I-SceI enzyme they used to create chromosome breaks could cut DNA at  as surprising number of previously unrecognized locations across the genome, information that could impact the enzyme’s utility as a tool for gene therapy. “We think that HTGTS could help the gene therapy community better understand the full activity of the enzymes they are considering and avoid possible off-target effects,” Alt said.

The study was supported by the National Cancer Institute, the National Institute of Allergy and Infectious Disease, the Howard Hughes Medical Institute, the Leukemia and Lymphoma Society, and the V Foundation.

Erin McColgan
Children's Hospital Boston

Children’s Hospital Boston is home to the world’s largest research enterprise based at a pediatric medical center, where its discoveries have benefited both children and adults since 1869. More than 1,100 scientists, including nine members of the National Academy of Sciences, 11 members of the Institute of Medicine and nine members of the Howard Hughes Medical Institute comprise Children’s research community. Founded as a 20-bed hospital for children, Children’s Hospital Boston today is a 396 bed comprehensive center for pediatric and adolescent health care grounded in the values of excellence in patient care and sensitivity to the complex needs and diversity of children and families. Children’s also is the primary pediatric teaching affiliate of Harvard Medical School. For more information about research and clinical innovation at Children’s, visit:

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