A DNA Microarray-Based Genetic Screen for Nonhomologous End-Joining Mutants in Saccharomyces cerevisiae

Author:

Ooi Siew Loon1,Shoemaker Daniel D.2,Boeke Jef D.1

Affiliation:

1. Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 617 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.

2. Rosetta Inpharmatics Inc., 12040 115th Street Avenue Northeast, Kirkland, WA 98034, USA.

Abstract

We describe a microarray-based screen performed by imposing different genetic selections on thousands of yeast mutants in parallel, representing most genes in the yeast genome. The presence or absence of mutants was detected by oligonucleotide arrays that hybridize to 20-nucleotide “barcodes.” We used this method to screen for components of the nonhomologous end-joining (NHEJ) pathway. Known components of the pathway were identified, as well as a gene not previously known to be involved in NHEJ, NEJ1 . Nej1 protein interacts with the amino terminus of LIF1/XRCC4, a recently recognized “guardian of the genome” against cancer.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference27 articles.

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3. The UPTAG and DOWNTAG features allow large numbers of deletion strains to be pooled and analyzed in parallel. The pool of mutants was transformed with either circular or Eco RI–linearized pRS416 and plated onto SC-Ura plates. Genomic DNA was isolated from pooled Ura + transformants and used as a PCR template to amplify the DOWNTAGs or UPTAGs of the strains present. Genomic DNA from the circular pRS416-transformed cells was amplified with Cy5 (red)-labeled universal primer whereas that of the Eco RI–linearized pRS416-transformed cells was amplified with Cy3 (green)-labeled universal primers. These fluorescently labeled probes were then cohybridized to a DNA microarray bearing each tag in triplicate. An NHEJ-defective deletion strain would be underrepresented in the Eco RI–linearized plasmid-transformed pool and would have a reduced signal in the Cy3 channel (Web fig. 1B).

4. Genomic profiling of drug sensitivities via induced haploinsufficiency

5. Chromosomal stability and the DNA double-stranded break connection

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