DNA repair mapped, systems-wide

Scientists use sweeping approach to generate map of interconnected cellular responses to DNA damage

By | May 19, 2006

Many cellular processes -- including DNA replication and repair, cell cycle control, metabolism, and stress responses -- form an integrated response to DNA damage, according to a report in this week's Science. The authors used a systems biology approach to create a map of transcriptional networks that are activated when yeast DNA is damaged. "We now know an order of magnitude more pathway connections than were known before, as far as how information is transmitted through the cell in response to damage," senior author Trey Ideker of the University of California, San Diego, told The Scientist. Looking at cellular processes from a wide-angle view -- rather than the one-gene, one-protein approach of classical biology -- permits the construction of "a complete wiring diagram" of transcriptional interactions, Ideker said, which will help scientists control cellular response to DNA damage. Scientists have gathered significant data about how DNA damage is sensed and repaired in the cell, Ideker explained, and previous work has shown that many pathways other than classic "repair" pathways become activated after damage. "What's been entirely unknown is how those different pathways are interlinked to form one cohesive response," Ideker said. Ideker and his colleagues -- led by Christopher T. Workman and H. Craig Mak, also at UCSD -- first screened yeast cells for transcription factors involved in the cellular response to an alkylation agent called methyl-methanesulfonate (MMS). The researchers found 30 transcription factors that appeared to be involved in the damage response -- either because their expression changed with MMS treatment, they bound to promoters of genes whose expression changed with MMS treatment, or their deletion diminished a cell's ability to recover from damage. The authors then used a technique called ChIP-chip -- chromatin immunoprecipitation combined with microarray chip hybridization -- to identify the transcriptional network that each of the 30 transcription factors induces when exposed to MMS. By comparing the genes and protein-DNA interactions after MMS treatment to interactions under normal growth conditions, the authors mapped how transcription factors change their behavior when the cell experiences DNA damage. These changes include employing different DNA binding motifs, altering regulated genes, or changing pairings with other transcription factors. Ideker and his colleagues next used microarrays of yeast genetic knockouts to determine how deleting a key transcription factor changes gene expression induced by MMS. If the ChIP-chip analysis showed that a transcription factor binds to promoters of a certain set of genes, the authors reason, then knocking out that transcription factor should alter those genes' response to MMS treatment. Since transcription factors can also affect genes that they don't bind directly, however, the authors also applied a Bayesian modeling technique to determine likely intermediate factors through which transcription factors modulate downstream gene activity. The resulting transcriptional network shows how transcription factors regulate the expression of 82 genes in response to MMS damage. At the core of the network lies a set of known DNA damage response genes, but surrounding these genes are interacting networks involved in DNA replication and repair, cell cycle arrest, stress responses, and metabolic pathways. "We've now explained all of these pathways that people have hinted at before within the context of one circuit diagram," Ideker said. "I really liked the concept of the paper," said Yolanda Sanchez of Dartmouth Medical School in Hanover, NH, who was not involved in the study. "They took a lot of information that was already out there... and figured out connections between the pathways." In future studies, it will be important to add analyses of post-transcriptional and post-translational mechanisms to what they've revealed about transcriptional pathways, Sanchez added. "I'm sure that's coming." "They certainly uncovered some novel connections and pathways that weren't known before," said Grant Brown of the University of Toronto in Ontario. "The biology is not followed up in any rigorous sense, but the point of this is to generate novel ideas that then lead to more hypothesis-driven experiments." mphillips@the-scientist.com Links within this article C.T. Workman et al., "A systems approach to mapping DNA damage response pathways," Science, May 19, 2006. http://www.sciencemag.org M.B. Castan, "DNA damage responses: Cancer and beyond," The Scientist, October 10, 2005. https://www.the-scientist.com/article/display/15766/ Trey Ideker http://chianti.ucsd.edu/idekerlab/index.html J.F. Wilson, "Elucidating the DNA damage pathway," The Scientist, January 21, 2002. https://www.the-scientist.com/article/display/12816/ S.A. Jelinsky, L.D. Samson, "Global response of Saccharomyces cerevisiae to an alkylating agent," PNAS, February 16, 1999. PM_ID: 9990050 Yolanda Sanchez http://www.dartmouth.edu/~sanchezlab/ Grant Brown http://biochemistry.utoronto.ca/brown/

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