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Selected publications from the Brewer/Raghu lab

Brewer BJ, Dunham MJ, Raghuraman MK (2024) A unifying model that explains the origins of human inverted copy number variants. PLoS Genet 20(1): e1011091.

Martin R, Espinoza CY, Large CRL, Rosswork J, Van Bruinisse C, Miller AW, et al. (2024) Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. PLoS Genet 20(1): e1010850.

Kwan, E. X., Alvino, G. M., Lynch, K. L., Levan, P. F., Amemiya, H. M., Wang, X. S., Johnson, S. A., Sanchez, J. C., Miller, M. A., Croy, M., Lee, S. B., Naushab, M., Bedalov, A., Cuperus, J. T., Brewer, B. J., Queitsch, C., & Raghuraman, M. K. (2023). Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast. Cell Reports42:112161.

Hoerr, R. E., Eng, A., Payen, C., Di Rienzi, S. C., Raghuraman, M. K., Dunham, M. J., Brewer, B. J., & Friedman, K. L. (2023). Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions. Genetics, iyad010. Advance online publication.

Lynch, K. L., Alvino, G. M., Kwan, E. X., Brewer, B. J., and Raghuraman, M. K. (2019). The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast. PLoS Genet 15(10): e1008430.

Sanchez, J. C., Ollodart, A., Large, C. R. L., Clough, C., Alvino, G. M., Tsuchiya, M., Crane, M., Kwan, E. X., Kaeberlein, M., Dunham, M. J., Raghuraman, M. K., and Brewer, B. J. (2019). Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae. Genetics 213:229-249.

Sanchez, J.C., Kwan, E.X., Pohl, T.J., Amemiya, H.M., Raghuraman, M.K., and Brewer, B.J. (2017). Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. PLoS Genet 13, e1007041.

Kwan, E. X., Wang, X. S., Amemiya, H. M., Brewer, B. J., and Raghuraman, M. K. (2016). rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants. G3: Genes, Genomes, Genetics 6:2829-2838. Featured in the 2016 issue of the GSA Journals Spotlight.

Brewer, B.J., Payen, C., Di Rienzi, S.C., Higgins, M.M., Ong, G., Dunham, M.J., and Raghuraman, M.K. (2015). Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. PLoS Genet 11, e1005699.

Hiraga, S., Alvino, G. M., Chang, F.-J., Lian, H. Y., Sridhar, A., Kubota, T., Brewer, B. J., Weinreich, M., Raghuraman, M. K., and Donaldson, A. D. (2014).  Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex.  Genes Dev. 28:372-383.

Peng, J., Raghuraman, M.K., and Feng, W. (2014). Analysis of replication timing using synchronized budding yeast cultures. Methods Mol Biol 1170, 477-499.

Peng, J., Raghuraman, M.K., and Feng, W. (2014). Analysis of ssDNA gaps and DSBs in genetically unstable yeast cultures. Methods Mol Biol 1170, 501-515.

Liachko, I., Youngblood, R.A., Tsui, K., Bubb, K.L., Queitsch, C., Raghuraman, M.K., Nislow, C., Brewer, B.J., and Dunham, M.J. (2014). GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris. PLoS Genet 10:e1004169.

Payen, C., Di Rienzi, S.C., Ong, G.T., Pogachar, J.L., Sanchez, J.C., Sunshine, A.B., Raghuraman, M.K., Brewer, B.J., Dunham, M.J. (2014). The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection. G3: Genes, Genomes, Genetics 4:399-409.

Pohl, T. J., Kolor, K., Fangman, W. L., Brewer, B. J., and Raghuraman, M. K. (2013). A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics 3:1955-1963.

Kwan, E. X., Foss, E. J., Tsuchiyama, S., Alvino, G. M., Kruglyak, L., Kaeberlein, M., Raghuraman, M. K., Brewer, B. J., Kennedy, B. K., and Bedalov, A. (2013). A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan. PLoS Genet 9:e1003329.

Di Rienzi, S. C., Lindstrom, K. C., Mann, T., Noble, W. S., Raghuraman, M. K., and Brewer, B. J. (2012). Maintaining replication origins in the face of genomic change. Genome Res. 22:1940-1952.

Pohl, T.J., Brewer, B.J., and Raghuraman, M.K. (2012). Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae. PLoS Genet 8:e1002677.

Feng, W., Di Rienzi, S., Raghuraman, M. K., and Brewer, B. J. (2011). Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation. G3: Genes, Genomes, Genetics 1:327-335.

Brewer, B.J., Payen, C., Raghuraman, M.K., and Dunham, M.J. (2011). Origin-Dependent Inverted-Repeat Amplification: A Replication-Based Model for Generating Palindromic Amplicons. PLoS Genet 7: e1002016.

Lian, H.Y., Robertson, E.D., Hiraga, S., Alvino, G.M., Collingwood, D., McCune, H.J., Sridhar, A., Brewer, B.J., Raghuraman, M.K., and Donaldson, A.D. (2011). The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation. Mol Biol Cell 22:1753-1765.

Supplementary material for Lian et al., 2011.

Di Rienzi, S.C., Lindstrom, K.C., Lancaster, R., Rolczynski, L., Raghuraman, M.K., and Brewer, B.J. (2011). Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii. Yeast 28:137-151.

L. waltii genome browser.

Supplemental information for Di Rienzi et al., 2011.

Raghuraman, M.K., and Brewer, B.J. (2010). Molecular analysis of the replication program in unicellular model organisms. Chromosome Res. 18:19-34.

Feng, W., Bachant, J., Collingwood, D., Raghuraman, M.K., and Brewer, B.J. (2009). Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress. Genetics 183:1249-1260.

Data supplement to Feng et al., 2009.

Di Rienzi, S., Collingwood, D., Raghuraman, M.K., and Brewer, B.J. (2009). Fragile Genomic Sites are Associated with Origins of Replication. Genome Biology and Evolution 1:350-363.

Data supplement to Di Rienzi et al., 2009.

McCune, H.J., Danielson, L.S., Alvino, G.M., Collingwood, D., Delrow, J.J., Fangman, W.L., Brewer, B.J., and Raghuraman, M.K. (2008). The Temporal Program of Chromosome Replication: Genomewide Replication in clb5∆ Saccharomyces cerevisiae. Genetics 180:1833-1847.

Data supplement to McCune et al., 2008.

Alvino, G.M., Collingwood, D., Murphy, J.M., Delrow, J., Brewer, B.J., and Raghuraman, M.K. (2007). Replication in hydroxyurea: it's a matter of time. Mol Cell Biol 27:6396-6406.

Data supplement to Alvino et al., 2007.

Feng, W., Collingwood, D., Boeck, M.E., Fox, L.A., Alvino, G.M., Fangman, W.L., Raghuraman, M.K., and Brewer, B.J. (2006). Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat Cell Biol 8:148-155.

Data supplement to Feng et al., 2006.

Raghuraman, M.K., Winzeler, E.A., Collingwood, D., Hunt, S., Wodicka, L., Conway, A., Lockhart, D.J., Davis, R.W., Brewer, B.J., and Fangman, W.L. (2001). Replication dynamics of the yeast genome. Science 294:115-121.

Data supplement to Raghuraman et al., 2001:

Raw data files
Pooled HL data (unsmoothed)
Pooled HL data (smoothed)
Trep data (smoothed)
Origin predictions
Replication profiles (pdf)