Goold HD, et al. (2025) Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome. Nat Commun 16(1):841 PMID:39833175
Zhou C, et al. (2024) The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging. Nat Commun 15(1):10139 PMID:39578428
Blount BA, et al. (2023) Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. Cell Genom 3(11):100418 PMID:38020971
Foo JL, et al. (2023) Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration. Cell Genom 3(11):100435 PMID:38020970
Lazar-Stefanita L, et al. (2023) Two differentially stable rDNA loci coexist on the same chromosome and form a single nucleolus. Proc Natl Acad Sci U S A 120(9):e2219126120 PMID:36821584
McCulloch LH, et al. (2023) Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. Cell Genom 3(11):100419 PMID:38020974
Schindler D, et al. (2023) Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 186(24):5237-5253.e22 PMID:37944512
Shen Y, et al. (2023) Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell Genom 3(11):100364 PMID:38020968
Williams TC, et al. (2023) Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Cell Genom 3(11):100379 PMID:38020977
Lazar-Stefanita L, et al. (2022) Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts. Cell Genom 2(8):None PMID:35983101
Valencia-Sánchez MI, et al. (2021) Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation. Science 371(6527) PMID:33479126
Agmon N, et al. (2020) Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast. Nucleic Acids Res 48(1):486-499 PMID:31745563
Chuang J, et al. (2018) Coupling Yeast Golden Gate and VEGAS for Efficient Assembly of the Violacein Pathway in Saccharomyces cerevisiae. Methods Mol Biol 1671:211-225 PMID:29170962
Hoggard TA, et al. (2018) Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins. PLoS Genet 14(5):e1007418 PMID:29795547
Pretorius IS and Boeke JD (2018) Yeast 2.0-connecting the dots in the construction of the world's first functional synthetic eukaryotic genome. FEMS Yeast Res 18(4) PMID:29648592
Zhao Y and Boeke JD (2018) Construction of Designer Selectable Marker Deletions with a CRISPR-Cas9 Toolbox in Schizosaccharomyces pombe and New Design of Common Entry Vectors. G3 (Bethesda) 8(3):789-796 PMID:29321167
Agmon N, et al. (2017) Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 114(8):E1470-E1479 PMID:28174266
Ikushima S and Boeke JD (2017) New Orthogonal Transcriptional Switches Derived from Tet Repressor Homologues for Saccharomyces cerevisiae Regulated by 2,4-Diacetylphloroglucinol and Other Ligands. ACS Synth Biol 6(3):497-506 PMID:28005347
Jiang S, et al. (2017) Construction of Comprehensive Dosage-Matching Core Histone Mutant Libraries for Saccharomyces cerevisiae. Genetics 207(4):1263-1273 PMID:29084817
Sliva A, et al. (2016) Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes. G3 (Bethesda) 6(4):881-92 PMID:26837954
Agmon N, et al. (2015) Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. ACS Synth Biol 4(7):853-9 PMID:25756291
Cai Y, et al. (2015) Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proc Natl Acad Sci U S A 112(6):1803-8 PMID:25624482
Ikushima S, et al. (2015) Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product. G3 (Bethesda) 5(10):1983-90 PMID:26206350
Lin Q, et al. (2015) RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth Biol 4(3):213-20 PMID:24895839
Mitchell LA, et al. (2015) Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res 43(13):6620-30 PMID:25956652
Simoneau A, et al. (2015) Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage. Genetics 200(1):185-205 PMID:25786853
Kuang Z, et al. (2014) High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol 21(10):854-63 PMID:25173176
Mitchell LA and Boeke JD (2014) Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proc Natl Acad Sci U S A 111(48):17003-10 PMID:25378705
Fiedler KL, et al. (2013) A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants. J Mass Spectrom 48(5):608-15 PMID:23674285
Ng TM, et al. (2013) Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics 195(3):795-807 PMID:24037263
Bheda P, et al. (2012) Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. Proc Natl Acad Sci U S A 109(16):E916-25 PMID:22474337
Darby MM, et al. (2012) The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. Mol Cell Biol 32(10):1762-75 PMID:22431520
Yarrington RM, et al. (2012) Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon. Genetics 190(2):523-35 PMID:22135353
Hyland EM, et al. (2011) An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes Dev 25(12):1306-19 PMID:21685365
Lin YY, et al. (2009) Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136(6):1073-84 PMID:19303850
Ben-Aroya S, et al. (2008) Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Mol Cell 30(2):248-58 PMID:18439903
Li F, et al. (2008) Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Mol Cell 30(3):325-35 PMID:18471978
Lin YY, et al. (2008) A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev 22(15):2062-74 PMID:18676811
Meluh PB, et al. (2008) Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods Mol Biol 416:221-47 PMID:18392971
Norris A, et al. (2008) Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction. PLoS Genet 4(12):e1000301 PMID:19079580
Pan X, et al. (2008) Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast'. FEMS Yeast Res 8(3):349-50
Qi Y, et al. (2008) Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18(12):1991-2004 PMID:18832443
Sulek M, et al. (2007) A critical role for the C-terminus of Nej1 protein in Lif1p association, DNA binding and non-homologous end-joining. DNA Repair (Amst) 6(12):1805-18 PMID:17765666
Yarrington RM, et al. (2007) Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains. J Virol 81(17):9004-12 PMID:17537863
Zurita-Martinez SA, et al. (2007) Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae. Genetics 176(4):2139-50 PMID:17565946
Celic I, et al. (2006) The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. Curr Biol 16(13):1280-9 PMID:16815704
Fry CJ, et al. (2006) The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Mol Cell Biol 26(23):9045-59 PMID:17015465
Gandhi TK, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38(3):285-93 PMID:16501559
Kastenmayer JP, et al. (2006) Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res 16(3):365-73 PMID:16510898
Takahashi H, et al. (2006) Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell 23(2):207-17 PMID:16857587
Bachman N, et al. (2005) TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev 19(8):955-64 PMID:15833918
Bolton EC, et al. (2005) Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon. RNA 11(3):308-22 PMID:15661848
Brannon AR, et al. (2005) Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain protein. Proc Natl Acad Sci U S A 102(8):2998-3003 PMID:15710895
Gelbart ME, et al. (2005) Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes Dev 19(8):942-54 PMID:15833917
Hyland EM, et al. (2005) Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol Cell Biol 25(22):10060-70 PMID:16260619
Peyser BD, et al. (2005) Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res 33(16):e140 PMID:16166654
Bachman N, et al. (2004) Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Genome Res 14(7):1232-47 PMID:15197163
Starai VJ, et al. (2004) A link between transcription and intermediary metabolism: a role for Sir2 in the control of acetyl-coenzyme A synthetase. Curr Opin Microbiol 7(2):115-9 PMID:15063846
Bolton EC and Boeke JD (2003) Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res 13(2):254-63 PMID:12566403
Irizarry RA, et al. (2003) Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Stat Appl Genet Mol Biol 2:Article1 PMID:16646779
Ooi SL, et al. (2003) DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat Genet 35(3):277-86 PMID:14566339
Starai VJ, et al. (2003) Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. Genetics 163(2):545-55 PMID:12618394
Lawler JF, et al. (2002) A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity. J Virol 76(1):346-54 PMID:11739699
Sandmeier JJ, et al. (2002) Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. Genetics 160(3):877-89 PMID:11901108
Carbrey JM, et al. (2001) Aquaporins in Saccharomyces: Characterization of a second functional water channel protein. Proc Natl Acad Sci U S A 98(3):1000-5 PMID:11158584
Lawler JF, et al. (2001) Frameshift signal transplantation and the unambiguous analysis of mutations in the yeast retrotransposon Ty1 Gag-Pol overlap region. J Virol 75(15):6769-75 PMID:11435555
Loewith R, et al. (2001) Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae. J Biol Chem 276(26):24068-74 PMID:11306585
Merkulov GV, et al. (2001) Ty1 proteolytic cleavage sites are required for transposition: all sites are not created equal. J Virol 75(2):638-44 PMID:11134277
Ooi SL, et al. (2001) A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 294(5551):2552-6 PMID:11701889
Sauve AA, et al. (2001) Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions. Biochemistry 40(51):15456-63 PMID:11747420
Kim JW, et al. (2000) Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants. Nucleic Acids Res 28(18):3666-73 PMID:10982890
Smith JS, et al. (2000) A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc Natl Acad Sci U S A 97(12):6658-63 PMID:10841563
Freeman-Cook LL, et al. (1999) The Schizosaccharomyces pombe hst4(+) gene is a SIR2 homologue with silencing and centromeric functions. Mol Biol Cell 10(10):3171-86 PMID:10512858
Smith JS, et al. (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19(4):3184-97 PMID:10082585
Winzeler EA, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285(5429):901-6 PMID:10436161
Brachmann CB, et al. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14(2):115-32 PMID:9483801
Kenna MA, et al. (1998) Invading the yeast nucleus: a nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo. Mol Cell Biol 18(2):1115-24 PMID:9448009
Kim JM, et al. (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8(5):464-78 PMID:9582191
Ooi SL, et al. (1998) Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA. RNA 4(9):1096-110 PMID:9740128
Smith JS, et al. (1998) Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. Genetics 149(3):1205-19 PMID:9649515
Lauermann V, et al. (1997) Increased length of long terminal repeats inhibits Ty1 transposition and leads to the formation of tandem multimers. Genetics 145(4):911-22 PMID:9093846
Nam K, et al. (1997) Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol Cell Biol 17(2):809-18 PMID:9001235
Devine SE and Boeke JD (1996) Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10(5):620-33 PMID:8598291
Vidal M, et al. (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci U S A 93(19):10315-20 PMID:8816797
Brachmann CB, et al. (1995) The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev 9(23):2888-902 PMID:7498786
Dollard C, et al. (1994) SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae. Mol Cell Biol 14(8):5223-8 PMID:8035801
Simchen G, et al. (1994) Mapping of DBR1 and YPK1 suggests a major revision of the genetic map of the left arm of Saccharomyces cerevisiae Chromosome XI. Genetics 138(2):283-7 PMID:7828812
Kawakami K, et al. (1993) A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics 135(2):309-20 PMID:8243996
Chapman KB, et al. (1992) SDH1, the gene encoding the succinate dehydrogenase flavoprotein subunit from Saccharomyces cerevisiae. Gene 118(1):131-6 PMID:1511876
Boeke JD, et al. (1991) Doubling Ty1 element copy number in Saccharomyces cerevisiae: host genome stability and phenotypic effects. Genetics 129(4):1043-52 PMID:1664403
Natsoulis G, et al. (1991) The products of the SPT10 and SPT21 genes of Saccharomyces cerevisiae increase the amplitude of transcriptional regulation at a large number of unlinked loci. New Biol 3(12):1249-59 PMID:1667480
Curcio MJ, et al. (1990) Ty RNA levels determine the spectrum of retrotransposition events that activate gene expression in Saccharomyces cerevisiae. Mol Gen Genet 220(2):213-21 PMID:2157950
Jacobs E, et al. (1988) Retrovirus-like vectors for Saccharomyces cerevisiae: integration of foreign genes controlled by efficient promoters into yeast chromosomal DNA. Gene 67(2):259-69 PMID:2844630
Trueheart J, et al. (1987) Two genes required for cell fusion during yeast conjugation: evidence for a pheromone-induced surface protein. Mol Cell Biol 7(7):2316-28 PMID:3302672
Boeke JD, et al. (1986) Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements. Mol Cell Biol 6(11):3575-81 PMID:3025601
Boeke JD, et al. (1984) A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet 197(2):345-6 PMID:6394957