The paper identifies a mechanism of gene amplification in yeast involving microhomology-mediated break-induced replication (mmBIR) at telomeres, leading to tandem duplication of chromosomal ends.

PLoS Genetics · Aug 20, 2026Peer-reviewedGenetics

Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA

Rebecca Martin, Claudia Y. Espinoza, Christopher R. L. Large, Joshua Rosswork, Cole Van Bruinisse, Aaron W. Miller, Joseph C. Sanchez, Madison A. Miller, Samantha Paskvan, Gina M. Alvino, Maitreya J. Dunham, M. K. Raghuraman, Bonita J. Brewer

The paper identifies a replication error mechanism called ODIRA that generates inverted copy number variants through template switching at replication forks, using yeast as a model system.

PLoS Genetics · Jan 4, 2024Peer-reviewedGenomics

Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains

Jie Peng, Ishita Joshi, Gina M. Alvino, Elizabeth X. Kwan, Wenyi Feng

The paper compares replication origin activation in two yeast strains under HU stress, identifying Rad53-dependent origins and showing differences in origin dynamics and checkpoint control.

PLoS ONE · Feb 14, 2022Peer-reviewedGenomics

Coordination of genome replication and anaphase entry by rDNA copy number in S. cerevisiae

Elizabeth X. Kwan, Gina M. Alvino, Kelsey L. Lynch, Paula F. Levan, Haley M. Amemiya, Xiaobin S. Wang, Sarah Johnson, Joseph C. Sanchez, Madison A. Miller, Mackenzie Croy, Seung‐been Lee, Maria Naushab, Josh T. Cuperus, Bonita J. Brewer, Christine Queitsch, M. K. Raghuraman

The paper shows that reducing rDNA copy number in S. cerevisiae changes its replication timing, delays genome replication, and links rDNA to cell cycle control via Cdc14p sequestration.

bioRxiv · Feb 25, 2021 · PreprintMolecular Biology

The limiting DNA replication initiation factors Sld2 and Sld3 influence origin efficiency independent of origin firing time

Kelsey L. Lynch, Elizabeth X. Kwan, Gina M. Alvino, Bonita J. Brewer, M. K. Raghuraman

This study shows that Sld2 and Sld3 abundance primarily affect origin efficiency in yeast replication, not firing time, using auxin-induced degradation.

PLoS Genetics · Oct 4, 2019Peer-reviewedMolecular Biology

Phenotypic and genotypic consequences of CRISPR/Cas9 editing of the replication origins in the rDNA of Saccharomyces cerevisiae

Joseph C. Sanchez, Anja R. Ollodart, Christopher R. L. Large, Courtnee A. Clough, Gina M. Alvino, Mitsuhiro Tsuchiya, Matthew M. Crane, Elizabeth X. Kwan, Matt R. Kaeberlein, Maitreya J. Dunham, M. K. Raghuraman, Bonita J. Brewer

This study edits rDNA replication origins in yeast using CRISPR/Cas9, revealing growth and lifespan consequences of such modifications.

Genetics · Jul 10, 2019Peer-reviewedGenetics