Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Genome-wide mapping of DNA strand breaks in Saccharomyces cerevisiae

DNA damage due to Reactive Oxygen Species (ROS) has severe consequences to cellular metabolism, and its accumulation can lead to many diseases. One type of ROS-induced DNA damage is produced primarily by hydroxyl radicals, which generate both single- and double-strand breaks in DNA. Our aim is to map the landscape of such damage on genome-wide scale at high resolution. A genome-wide map of ROS-induced DNA strand breaks is likely to show a greater amount of damage in open chromatin due to higher accessibility of genomic DNA in these regions.

In order to map oxidative damage throughout a genome at single-nucleotide resolution, we have developed a new method (OH-Seq) to biochemically process oxidatively damaged genomic DNA to make it suitable for high-throughput sequencing. We use gamma radiation to generate hydroxyl radicals in vivo and then process the damaged genomic DNA to tag the breaks with a sequencing adapter. By using Illumina high-throughput sequencing to locate such tagged sites in the genome, it is possible to obtain a high resolution genome wide map of DNA strand breaks. This map yields a detailed picture of functional regions and transcription factor binding sites in the genome, and has the potential to provide a new level of detail in the study of DNA repair and oxidatively-induced aging.

This research has been supported by the Ellison Medical Foundation.

Hari K. K. Subramanian1
Sarah E. Bernard1Cheryl Chiang1
Stephen C. J. Parker1
Thomas D. Tullius1, 3

1Department of Chemistry
Boston University
Boston, MA 02215, USA.
2NHGRI, NIH, Bethesda, MD 20892, USA. 3Program in Bioinformatics
Boston University
Boston, MA 02215, USA.

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