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Quantitative Analysis of the Rates for Repeat-Mediated Genome Instability in a Yeast Experimental System

  • Elina A. Radchenko
  • Ryan J. McGinty
  • Anna Y. Aksenova
  • Alexander J. Neil
  • Sergei M. MirkinEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1672)

Abstract

Instability of repetitive DNA sequences causes numerous hereditary disorders in humans, the majority of which are associated with trinucleotide repeat expansions. Here, we describe a unique system to study instability of triplet repeats in a yeast experimental setting. Using fluctuation assay and the novel program FluCalc we are able to accurately estimate the rates of large-scale expansions, as well as repeat-mediated mutagenesis and gross chromosomal rearrangements for different repeat sequences.

Key words

Trinucleotide repeats Repeat expansions Repeat-induced mutagenesis Fluctuation assay Expansion rate Mutation rate MSS-MLE FluCalc 

Notes

Acknowledgments

We thank Alexander A. Shishkin and Kartik A. Shah for their invaluable contributions in developing cassettes to study repeat instability, and for developing experimental protocols for the selection and PCR procedures, Timofei S. Bondarev for developing FluCalc program, and Durwood Marshall for statistical consulting. This study was funded by NIH grants GM105473 and GM60987 to S.M.M and RFBR grant #15-04-08658 and research project in the Centre for Molecular and Cell Technologies (Research Park, Saint-Petersburg State University) for A.Y.A.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Elina A. Radchenko
    • 1
  • Ryan J. McGinty
    • 1
  • Anna Y. Aksenova
    • 2
  • Alexander J. Neil
    • 1
  • Sergei M. Mirkin
    • 1
    Email author
  1. 1.Department of BiologyTufts UniversityMedfordUSA
  2. 2.Laboratory of Amyloid BiologySaint-Petersburg State UniversitySaint-PetersburgRussia

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