New Technique Identifies First Events in Translocations
A new genome-wide mapping method, translocation capture sequencing, identifies translocations in primary cells. the technique reveals that transcription favors chromosome rearrangement and the rearrangements define chromosome territories in B cells.
A novel technique that enables scientists to measure and document tumor-inducing changes in genomic DNA is providing new insight into the earliest events involved in the formation of leukemias, lymphomas and sarcomas, and could potentially lead to the discovery of ways to stop those events.
Rafael C. Casellas, Ph.D., senior investigator in the Genomics and Immunity Section at NIH’s National Institute of Arthritis and Musculoskeletal and Skin Diseases, working with Michel C. Nussenzweig, M.D., Ph.D., and his research team from the Rockefeller.University, and with support from Andre Nussenzweig, Ph.D., who heads NCI’s Laboratory of Genome Integrity at CCR, reported their findings in Cell.
The technology focuses on chromosomal rearrangements known as translocations. Translocations occur when a broken strand of DNA from one chromosome is erroneously joined with that of another chromosome. Although these irregularities can be beneficial in that they enable the immune system to respond to a vast number of microorganisms and viruses, they can also result in tumors.
Translocations can take place during the course of normal cell division, when each chromosome – a single strand of DNA containing many genes – is copied verbatim to provide genetic information for the daughter cells. Sometimes, during this process, byproducts of normal metabolism or other factors can cause breaks in the DNA. So the cell expresses specific enzymes whose primary purpose is to repair such lesions effectively, but when the enzymes mistakenly join pieces of two different chromosomes, the cell’s genetic information is changed.
The phenomenon is like breaking two sentences and then rejoining them incorrectly. For example, “the boy did his homework” and “the dog went to the vet” might become “the dog did his homework,” or “the boy went to the vet.” When a cell gets nonsensical information such as this, it can become deregulated and even malignant.
Scientists have known since the 1960s that recurrent translocations play a critical role in cancer. What was unclear was how these genetic abnormalities are created, since very few of them were studied, and only within the context of tumors. To better understand the nature of these tumor-inducing rearrangements, the authors had to create a system to visualize their appearance in normal, non-transformed cells.
The system the team created involved introducing enzymes that recognize and cause damage at a particular sequence in the DNA into cells from mice, thereby constructing a genome where a unique site is broken continuously. The group then used a technique called polymerase chain reaction (PCR) – which allows scientists to quickly amplify short sequences of DNA – to check all the sites in the genome that would get translocated to this particular break.
Using this technique, they were able to examine more than 180,000 chromosomal rearrangements from 400 million white blood cells, called B cells. Based on this large data set, the scientists were able to make several important observations about the translocation process. For one, they learned that most of the translocations involve gene domains, rather than intergenic DNA (or the space on the DNA between the genes). They also found that most translocations target active genes, with a clear bias for the beginning of the gene, as opposed to its middle or end. The team also showed that a particular enzyme that normally creates DNA breaks in B cells, dramatically increases the incidence of translocations during the immune response. This feature explains the long-standing observation that more than 95 percent of human lymphomas and leukemias are of B cell origin.Summary Posted: Sat, 10/01/2011
Translocation-Capture Sequencing Reveals the Extent and Nature of Chromosomal Rearrangements in B Lymphocytes http://www.sciencedirect.com/science/article/pii/S0092867411009998 Reviewed by Donna Kerrigan