Publications
*Co-first authors; †Corresponding author
2025
Mistranslating tRNA variants impact the proteome and phosphoproteome of Saccharomyces cerevisiae
Berg MD†, Chang AT, Rodriguez-Mias RA, Villén J†
G3: Genes, Genomes, Genetics. In press (2025)
R2HaPpY: Rapid-robust phosphotyrosine peptide enrichment using HaloTag-Src SH2 pY superbinder
Chang A, Rodriguez-Mias RA, Berg MD, Moggridge S, Villén J
bioRxiv (2025)
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
Wen B, Hsu C, Shteynberg D, Zeng W-F, Riffle M, Chang A, Mudge MC, Nunn BL, MacLean BX, Berg MD, Villén J, MacCoss MJ, Noble WS
Nat Commun. 16(1):9815 (2025)
TUDCA modulates drug availability to regulate resistance to acute ER stress in Saccharomyces cerevisiae
Chadwick SR, Stack-Couture S, Berg MD, Di Gregorio S, Lung B, Genereaux J, Moir RD, Brandl CJ, Willis IM, Snapp EL, Lajoie P
Mol Biol Cell. 35(2):ar13 (2025)
2024
High-throughput identification of calcium regulated proteins across diverse proteomes
Locke TM, Fields R, Gizinski H, Otto GM, MacEwen MJS, Rusnac D-V, He P, Shechner DM, McGann CD, Berg MD, Villén J, Sancak Y, Schweppe DK
Cell Reports. 43(11):114879 (2024)
Mistranslating tRNA variants have anticodon- and sex-specific impacts on Drosophila melanogaster
Isaacson JR, Berg MD, Jagiello J, Yeung W, Charles B, Villén J, Brandl CJ, Moehring AJ
G3: Genes, Genomes, Genetics. 14(12):jkae230 (2024)
- Selected as a featured article and highlighted in the Genes to Genomes blog
Impact of tRNA-induced proline-to-serine mistranslation on the transcriptome of Drosophila melanogaster
Isaacson JR, Berg MD, Yeung W, Villén J, Brandl CJ, Moehring AJ
G3: Genes, Genomes, Genetics. 14(9):jkae151 (2024)
2023
Anticodon sequence determines the impact of mistranslating tRNAAla variants
Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD†
RNA Biol. 20(1):791-804 (2023)
Analysis of financial challenges faced by graduate students in Canada
Laframboise SJ, Bailey T, D A-T, Rose M, Zhou Z, Berg MD, Holland S, Abdul SA, O’Connor K, El-Sahli S, Boucher DM, Fairman G, Deng J, Shaw K, Noblett N, D’Addario A, Empey M, Sinclair K
Biochem Cell Biol. 101(4):326-360 (2023)
Tra1 controls the transcriptional landscape of the aging cell
Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P
G3: Genes, Genomes, Genetics. 13(1):jkac287 (2023)
2022
Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG
Berg MD†, Zhu Y, Loll-Krippleber R, San Luis B-J, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ†
G3: Genes, Genomes, Genetics. 12(7):jkac125 (2022)
A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects
Isaacson JR, Berg MD, Charles B, Jagiello J, Villén J, Brandl CJ, Moehring AJ
G3: Genes, Genomes, Genetics. 12(5):jkac035 (2022)
2021
Regulating expression of mistranslating tRNAs by readthrough RNA polymerase II transcription
Berg MD†, Isaacson JR, Cozma E, Genereaux J, Lajoie P, Villén J, Brandl CJ†
ACS Synth Biol. 10(11):3177-3189 (2021)
The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis
Razzaq I*, Berg MD*, Jiang Y, Genereaux J, Uthayakumar D, Kim GH, Agyare-Tabbi M, Halder V, Brandl CJ, Lajoie P, Shapiro RS
GENETICS. 219(2):iyab131 (2021)
The amino acid substitution affects cellular response to mistranslation
Berg MD†*, Zhu Y*, Ruiz BY, Loll-Krippleber R, Isaacson J, San Luis B-J, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ†
G3: Genes, Genomes, Genetics. 11(10):jkab218 (2021)
2020
Chemical-genetic interactions with the proline analog L-azetidine-2-carboxylic acid in Saccharomyces cerevisiae
Berg MD†, Zhu Y, Isaacson J, Genereaux J, Loll-Krippleber R, Brown GW, Brandl CJ†
G3: Genes, Genomes, Genetics. 10(12):4335-4345 (2020)
Transfer RNAs: Diversity in form and function
Berg MD† and Brandl CJ
RNA Biol. 18(3):316-339 (2020)
Mistranslating tRNA identifies a deleterious S213P mutation in the Saccharomyces cerevisiae eco1-1 allele
Zhu Y*, Berg MD*, Yang P, Loll-Krippleber R, Brown GW, Brandl CJ
Biochem Cell Biol. 98(5):624-630 (2020)
2019
Modulating mistranslation potential of tRNASer in Saccharomyces cerevisiae
Berg MD†, Zhu Y, Genereaux J, Ruiz BY, Rodriguez-Mias RA, Allan T, Bahcheli A, Villén J, Brandl CJ†
GENETICS. 213(3):849-863 (2019)
- Selected as a highlighted article
Targeted sequencing reveals expanded genetic diversity of human transfer RNAs
Berg MD†, Giguere DJ, Dron JS, Lant JT, Genereaux J, Liao C, Wang J, Robinson JF, Gloor GB, Hegele RA, O’Donoghue P, Brandl CJ
RNA Biol. 16(11):1574-1585 (2019)
- Highlighted by Western University Schulich School of Medicine & Dentistry
- Covered in phys.org article and other news outlets
Sfp1 links TORC1 and cell growth regulation to the yeast SAGA-complex component Tra1 in response to polyQ proteotoxicity
Jiang Y, Berg MD, Genereaux J, Ahmed K, Duennwald ML, Brandl CJ, Lajoie P
Traffic. 20(4):267-283 (2019)
Pathways to disease from natural variations in human cytoplasmic tRNAs
Lant JT, Berg MD, Heinemann IU, Brandl CJ, O’Donoghue P
J Biol Chem. 294(14):5294-5308 (2019)
2018
Acceptor stem differences contribute to species-specific use of yeast and human tRNASer
Berg MD†, Genereaux J, Zhu Y, Mian S, Gloor GB, Brandl CJ†
Genes. 9(12):E612 (2018)
The pseudokinase domain of Saccharomyces cerevisiae Tra1 is required for nuclear localization and incorporation into the SAGA and NuA4 complexes
Berg MD†, Genereaux J, Karagiannis J, Brandl CJ†
G3: Genes, Genomes, Genetics. 8(6):1943-1957 (2018)
Visualizing tRNA-dependent mistranslation in human cells
Lant JT, Berg MD, Sze D, Hoffman KS, Turk M, Akinpelu I, Heinemann IU, Duennwald ML, Brandl CJ, O’Donoghue P
RNA Biol. 15(4-5):567-575 (2018)
2017
Evolving mistranslating tRNAs through a phenotypically ambivalent intermediate in Saccharomyces cerevisiae
Berg MD†, Hoffman KS, Genereaux J, Mian S, Trussler RS, Haniford DB, O’Donoghue P, Brandl CJ†
GENETICS. 206(4):1865-1879 (2017)
- Selected as a highlighted article and featured on the Saccharomyces Genome Database blog
Genetic selection for mistranslation rescues a defective co-chaperone in yeast
Hoffman KS, Berg MD, Shilton BH, Brandl CJ, O’Donoghue P
Nucleic Acids Res. 45(6):3407-3421 (2017)