Literature DB >> 29043640

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

Elina A Radchenko1, Ryan J McGinty1, Anna Y Aksenova2, Alexander J Neil1, Sergei M Mirkin3.   

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.

Entities:  

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

Mesh：

Year:  2018        PMID： 29043640      PMCID： PMC5741187          DOI： 10.1007/978-1-4939-7306-4_29

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  19 in total

Review 1.  Determining mutation rates in bacterial populations.

Authors:  W A Rosche; P L Foster
Journal:  Methods       Date:  2000-01       Impact factor: 3.608

2.  On fluctuation analysis: a new, simple and efficient method for computing the expected number of mutants.

Authors:  S Sarkar; W T Ma; G H Sandri
Journal:  Genetica       Date:  1992       Impact factor: 1.082

3.  Methods for determining spontaneous mutation rates.

Authors:  Patricia L Foster
Journal:  Methods Enzymol       Date:  2006       Impact factor: 1.600

4.  Expansions, contractions, and fragility of the spinocerebellar ataxia type 10 pentanucleotide repeat in yeast.

Authors:  Nicole Cherng; Alexander A Shishkin; Lucas I Schlager; Ryan H Tuck; Laura Sloan; Robert Matera; Partha S Sarkar; Tetsuo Ashizawa; Catherine H Freudenreich; Sergei M Mirkin
Journal:  Proc Natl Acad Sci U S A       Date:  2011-01-31       Impact factor: 11.205

5.  A second look at the final number of cells in a fluctuation experiment.

Authors:  Qi Zheng
Journal:  J Theor Biol       Date:  2016-04-22       Impact factor: 2.691

6.  Large-scale expansions of Friedreich's ataxia GAA repeats in yeast.

Authors:  Alexander A Shishkin; Irina Voineagu; Robert Matera; Nicole Cherng; Brook T Chernet; Maria M Krasilnikova; Vidhya Narayanan; Kirill S Lobachev; Sergei M Mirkin
Journal:  Mol Cell       Date:  2009-07-10       Impact factor: 17.970

7.  Genome rearrangements caused by interstitial telomeric sequences in yeast.

Authors:  Anna Y Aksenova; Patricia W Greenwell; Margaret Dominska; Alexander A Shishkin; Jane C Kim; Thomas D Petes; Sergei M Mirkin
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

Review 8.  Expandable DNA repeats and human disease.

Authors:  Sergei M Mirkin
Journal:  Nature       Date:  2007-06-21       Impact factor: 49.962

Review 9.  The balancing act of DNA repeat expansions.

Authors:  Jane C Kim; Sergei M Mirkin
Journal:  Curr Opin Genet Dev       Date:  2013-05-29       Impact factor: 5.578

10.  Expansion of Interstitial Telomeric Sequences in Yeast.

Authors:  Anna Y Aksenova; Gil Han; Alexander A Shishkin; Kirill V Volkov; Sergei M Mirkin
Journal:  Cell Rep       Date:  2015-11-12       Impact factor: 9.423
View more
  18 in total

Review 1.  Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.

Authors:  Hannah L Klein; Giedrė Bačinskaja; Jun Che; Anais Cheblal; Rajula Elango; Anastasiya Epshtein; Devon M Fitzgerald; Belén Gómez-González; Sharik R Khan; Sandeep Kumar; Bryan A Leland; Léa Marie; Qian Mei; Judith Miné-Hattab; Alicja Piotrowska; Erica J Polleys; Christopher D Putnam; Elina A Radchenko; Anissia Ait Saada; Cynthia J Sakofsky; Eun Yong Shim; Mathew Stracy; Jun Xia; Zhenxin Yan; Yi Yin; Andrés Aguilera; Juan Lucas Argueso; Catherine H Freudenreich; Susan M Gasser; Dmitry A Gordenin; James E Haber; Grzegorz Ira; Sue Jinks-Robertson; Megan C King; Richard D Kolodner; Andrei Kuzminov; Sarah Ae Lambert; Sang Eun Lee; Kyle M Miller; Sergei M Mirkin; Thomas D Petes; Susan M Rosenberg; Rodney Rothstein; Lorraine S Symington; Pawel Zawadzki; Nayun Kim; Michael Lisby; Anna Malkova
Journal:  Microb Cell       Date:  2019-01-07

2.  Relocation of Collapsed Forks to the Nuclear Pore Complex Depends on Sumoylation of DNA Repair Proteins and Permits Rad51 Association.

Authors:  Jenna M Whalen; Nalini Dhingra; Lei Wei; Xiaolan Zhao; Catherine H Freudenreich
Journal:  Cell Rep       Date:  2020-05-12       Impact factor: 9.423

3.  Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans.

Authors:  Shelby J Priest; Marco A Coelho; Verónica Mixão; Shelly Applen Clancey; Yitong Xu; Sheng Sun; Toni Gabaldón; Joseph Heitman
Journal:  PLoS Genet       Date:  2021-01-19       Impact factor: 5.917

4.  Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.

Authors:  Kehui Liu; Shanjun Deng; Chang Ye; Zeqi Yao; Jianguo Wang; Han Gong; Li Liu; Xionglei He
Journal:  Nat Methods       Date:  2021-12-02       Impact factor: 28.547

5.  Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans.

Authors:  Vikas Yadav; Cullen Roth; Shelby J Priest; Tim A Dahlmann; Ulrich Kück; Paul M Magwene; Joseph Heitman
Journal:  Nat Microbiol       Date:  2022-08-02       Impact factor: 30.964

6.  Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes.

Authors:  Natalie A Lamb; Jonathan E Bard; Raphael Loll-Krippleber; Grant W Brown; Jennifer A Surtees
Journal:  Genetics       Date:  2022-07-30       Impact factor: 4.402

7.  Partners in crime: Tbf1 and Vid22 promote expansions of long human telomeric repeats at an interstitial chromosome position in yeast.

Authors:  Elina A Radchenko; Anna Y Aksenova; Kirill V Volkov; Alexander A Shishkin; Youri I Pavlov; Sergei M Mirkin
Journal:  PNAS Nexus       Date:  2022-06-08

8.  Rad9-mediated checkpoint activation is responsible for elevated expansions of GAA repeats in CST-deficient yeast.

Authors:  Ekaterina Spivakovsky-Gonzalez; Erica J Polleys; Chiara Masnovo; Jorge Cebrian; Adrian M Molina-Vargas; Catherine H Freudenreich; Sergei M Mirkin
Journal:  Genetics       Date:  2021-10-02       Impact factor: 4.402

9.  Characterization of systemic genomic instability in budding yeast.

Authors:  Nadia M V Sampaio; V P Ajith; Ruth A Watson; Lydia R Heasley; Parijat Chakraborty; Aline Rodrigues-Prause; Ewa P Malc; Piotr A Mieczkowski; Koodali T Nishant; Juan Lucas Argueso
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-26       Impact factor: 11.205

10.  Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations.

Authors:  Milo S Johnson; Shreyas Gopalakrishnan; Juhee Goyal; Megan E Dillingham; Christopher W Bakerlee; Parris T Humphrey; Tanush Jagdish; Elizabeth R Jerison; Katya Kosheleva; Katherine R Lawrence; Jiseon Min; Alief Moulana; Angela M Phillips; Julia C Piper; Ramya Purkanti; Artur Rego-Costa; Michael J McDonald; Alex N Nguyen Ba; Michael M Desai
Journal:  Elife       Date:  2021-01-19       Impact factor: 8.140
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.