# Bonita J. Brewer
**Bonita "Bonny" J. Brewer** is a professor of genome sciences at the University of Washington, known for her work on the origins and timing of eukaryotic [DNA replication](https://www.edgepedia.org/dna-replication) in the budding yeast *Saccharomyces cerevisiae*.[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) Her research asks how a cell duplicates its chromosomes once, and only once, per cell cycle: replication starts at multiple origins that fire at different times during S phase, and her lab studies how cells choose which origins to use, when they fire, and how they respond when replication is stressed.[2](https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/) • [3](https://fangman-brewer.genetics.washington.edu/)
| Key facts | |
|---|---|
| Position | Professor of Genome Sciences, University of Washington[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) |
| Field | Molecular biology; eukaryotic DNA replication origins and replication timing[3](https://fangman-brewer.genetics.washington.edu/) |
| Training | B.S. in biology and mathematics education, University of Missouri; doctorate in genetics, University of Washington[2](https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/) |
| Signature work | "The localization of replication origins on ARS plasmids in *S. cerevisiae*", *Cell*, 1987[4](https://fangman-brewer.genetics.washington.edu/publications.html) |
| Techniques pioneered | Two-dimensional gel electrophoresis for mapping origins; early genome-wide microarray methods for replication[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) |
| Main funding | NIH R01 GM018926 (NIGMS), project years 1976 to 2013[5](https://grantome.com/grant/NIH/R01-GM018926-40) |
| Honor | Fellow of the AAAS, named January 2010[2](https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/) |
| Most recent paper | First author, *PLOS Genetics*, August 20, 2026[6](https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1012214) |
## Career and training
Brewer earned a B.S. degree in biology and mathematics education at the [University of Missouri](https://www.edgepedia.org/university-of-missouri) and taught high school biology before receiving a doctorate in genetics from the University of Washington.[2](https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/) Her research at Washington is conducted in her laboratory.[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) • [3](https://fangman-brewer.genetics.washington.edu/) In January 2010 she was among about 400 new Fellows of the [American Association for the Advancement of Science](https://www.edgepedia.org/american-association-for-the-advancement-of-science) (AAAS) announced by the society.[2](https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/)
## Representative work
Her 1987 *Cell* paper, "The localization of replication origins on ARS plasmids in *S. cerevisiae*", mapped where replication begins on plasmids carrying ARS elements; it was published in *Cell* 51(3): 463–471.[4](https://fangman-brewer.genetics.washington.edu/publications.html)
## Genome-wide origin mapping
Nearly 50 years ago her lab pioneered two-dimensional gel electrophoresis techniques to map specific replication origins and to determine the efficiency with which they are activated; in the early days of DNA microarrays it developed methods and algorithms to study replication on a genome-wide scale.[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) A 2001 *Science* paper, "Replication dynamics of the yeast genome" (*Science* 294: 115–121, October 5, 2001), applied those genome-wide methods to locate replication origins across the yeast chromosomes.[4](https://fangman-brewer.genetics.washington.edu/publications.html)
Several of her papers shaped how origins are understood. A 1993 *Science* study showed that two ARS elements 6.5 kilobase pairs apart interfere with each other: replication initiates from one or the other with equal probability, but rarely, under 5 percent of the time, from both on the same DNA molecule; the paper notes that eukaryotic origins are spaced an average of 50 to 100 kilobase pairs apart.[7](https://doi.org/10.1126/science.8259517) Her 1992 *Cell* review, "A question of time: Replication origins of eukaryotic chromosomes", drew together the evidence that origins fire at characteristic times in S phase, including the findings that yeast centromeres replicate early and telomeres late, and that the time of origin activation is subject to position effects.[8](https://doi.org/10.1016/0092-8674(92)90505-7) In a 1994 review she proposed that the strong sequence dependence of replication initiation seen in lower eukaryotes may be a by-product of the small size of their intergenic sequences rather than a general mechanistic requirement, noting that most eukaryotic origins lie in intergenic spacers.[9](https://www.sciencedirect.com/science/article/abs/pii/S0959437X05800450)
Her single-author 1988 *Cell* paper, "When polymerases collide: replication and the transcriptional organization of the *E. coli* chromosome" (*Cell* 53(5): 679–686), according to the paper itself, examined how the bacterial replication machinery interacts with the chromosome's transcriptional organization.[10](https://europepmc.org/article/MED/3286014)
## Later work and current research
Later aims of her NIH grant asked whether replication origins are intrinsically destabilizing elements in the genome, using evolutionary comparisons of *S. cerevisiae* with its distant relative *Kluyveromyces waltii* (now *Lachancea waltii*).[5](https://grantome.com/grant/NIH/R01-GM018926-40) • [3](https://fangman-brewer.genetics.washington.edu/) The lab also studies genome instability arising from replication itself. Growing yeast continuously for many weeks in chemostats limited for sulfur invariably amplifies *SUL1*, the gene encoding the primary sulfate transporter.[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) A 2011 *PLoS Genetics* paper proposed origin-dependent inverted-repeat amplification as a replication-based model for generating palindromic amplicons.[4](https://fangman-brewer.genetics.washington.edu/publications.html) A 2019 *PLOS Genetics* study tested how manipulating levels of replication initiation factors affects origin firing efficiency in yeast.[11](https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1008430)
## Recent developments
Brewer has remained active. Her selected publications include a 2024 *PLoS Genetics* paper, "A unifying model that explains the origins of human inverted copy number variants", extending the amplification work to human genome rearrangements.[1](https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/) In 2025 the lab published "rDNA copy number variation affects yeast fitness in response to different environments" in *Genetics* (230: iyaf075), and manuscripts submitted April 17, 2026 cover *SUL1*/Y' telomeric amplicons and rDNA instability in aging yeast.[4](https://fangman-brewer.genetics.washington.edu/publications.html) On August 20, 2026, *PLOS Genetics* published her first-author paper showing that telomeric amplicons of *SUL1* and Y' in yeast are generated by microhomology-mediated break induced replication occurring in cis (*PLoS Genet* 22(8): e1012214), with her affiliation given as the Department of Genome Sciences, University of Washington, Seattle.[6](https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1012214)
## References
1. Bonny Brewer – UW Genome Sciences. https://www.gs.washington.edu/about/directory/faculty/bonny-brewer/
2. Six UW researchers named Fellows of AAAS – UW News. https://www.washington.edu/news/2010/01/07/six-uw-researchers-named-fellows-of-aaas/
3. Brewer/Raghuraman Lab Home Page. https://fangman-brewer.genetics.washington.edu/
4. B-R lab publications. https://fangman-brewer.genetics.washington.edu/publications.html
5. Eukaryotic Chromosome Replication – Bonita Brewer (NIH R01 GM018926-40). https://grantome.com/grant/NIH/R01-GM018926-40
6. Brewer BJ, et al. (2026) Telomeric amplicons of SUL1 and Y' in yeast are generated by microhomology-mediated break induced replication occurring in cis. PLoS Genet 22(8): e1012214. https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1012214
7. Initiation at Closely Spaced Replication Origins in a Yeast Chromosome (Science, 1993). https://doi.org/10.1126/science.8259517
8. https://doi.org/10.1016/0092-8674(92)90505-7
9. Intergenic DNA and the sequence requirements for replication initiation in eukaryotes (Current Opinion in Genetics & Development, 1994). https://www.sciencedirect.com/science/article/abs/pii/S0959437X05800450
10. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome (Cell, 1988). https://europepmc.org/article/MED/3286014
11. The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast (PLOS Genetics, 2019). https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1008430
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in genetics, genomics, and genome engineering › DNA repair and genome stability*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026 · Edited: Sep 25, 2026; Oct 11, 2026; Oct 15, 2026 · Last review: Sep 25, 2026*
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License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license