Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae in University Park, Florida, United States
Locale: University Park, Florida, United States
Topic: saccharomyces cerevisiae
- Esakova O, Perederina A, Berezin I, Krasilnikov A. Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate. Nucleic Acids Res. 2013;41:7084-91 pubmed publisher..Implications for the structural organization of RNase MRP and the roles of its components are discussed. ..
- Vallieres C, Holland S, Avery S. Mitochondrial Ferredoxin Determines Vulnerability of Cells to Copper Excess. Cell Chem Biol. 2017;24:1228-1237.e3 pubmed publisher..The data indicate that the essential mitochondrial ferredoxin is an important copper target, determining a tipping point where plentiful copper supply becomes excessive. This knowledge could help in tackling copper-related diseases. ..
- Grant P, Duggan L, Cote J, Roberts S, Brownell J, Candau R, et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997;11:1640-50 pubmed..e., tbp). ..
- Maupin Furlow J, Ferry J. A proteasome from the methanogenic archaeon Methanosarcina thermophila. J Biol Chem. 1995;270:28617-22 pubmed..The results suggest that proteasomes are more widespread in the Archaea than previously proposed. Southern blotting experiments suggested the presence of ubiquitin-like sequences in M. thermophila. ..
- Cote J, Quinn J, Workman J, Peterson C. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994;265:53-60 pubmed..A direct ATP-dependent interaction between the SWI/SNF complex and nucleosomal DNA was detected. These observations suggest that a primary role of the SWI/SNF complex is to promote activator binding to nucleosomal DNA. ..
- Jiang C, Pugh B. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol. 2009;10:R109 pubmed publisher..Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/. ..
- Koerber R, Rhee H, Jiang C, Pugh B. Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol Cell. 2009;35:889-902 pubmed publisher..These findings suggest that nucleosomes around promoter regions have position-specific functions and that some gene regulators have position-specific nucleosomal interactions. ..
- Kehoe S, Heinrichs A, Baumrucker C, Greger D. Effects of nucleotide supplementation in milk replacer on small intestinal absorptive capacity in dairy calves. J Dairy Sci. 2008;91:2759-70 pubmed publisher..Supplementation of nucleotides derived from yeast tended to increase calf intestinal function, provide a more beneficial intestinal environment, and improve intestinal morphology. ..
- Tomar R, Zheng S, Brunke Reese D, Wolcott H, Reese J. Yeast Rap1 contributes to genomic integrity by activating DNA damage repair genes. EMBO J. 2008;27:1575-84 pubmed publisher..We propose that Rap1 acts as a rheostat controlling nucleotide pools in response to shortened telomeres and DNA damage, providing a mechanism for fine-tuning the RNR genes during checkpoint activation. ..
- Huisinga K, Pugh B. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell. 2004;13:573-85 pubmed..These two distinct modes of transcription regulation might reflect the need to balance inducible stress responses with the steady output of housekeeping genes. ..
- Grant P, Schieltz D, Pray Grant M, Steger D, Reese J, Yates J, et al. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell. 1998;94:45-53 pubmed..These results illustrate a role for certain TAF(II) proteins in the regulation of gene expression at the level of chromatin modification that is distinct from the TFIID complex and TAF(II)145. ..
- Grant P, Schieltz D, Pray Grant M, Yates J, Workman J. The ATM-related cofactor Tra1 is a component of the purified SAGA complex. Mol Cell. 1998;2:863-7 pubmed..These results indicate a role for Tra1 in the regulation of transcriptional activation through the recruitment of HAT activity to an activator-bound promoter. ..
- Gavin I, Kladde M, Simpson R. Tup1p represses Mcm1p transcriptional activation and chromatin remodeling of an a-cell-specific gene. EMBO J. 2000;19:5875-83 pubmed..We suggest that Tup1p can contribute to repression by blocking transcriptional activators, in addition to interacting with transcription machinery and stabilizing chromatin...
- Durant M, Pugh B. NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome. Mol Cell Biol. 2007;27:5327-35 pubmed..However, the deletion of BDF1 leads to the accumulation of Bdf2 at Bdf1-vacated sites. Thus, while Bdf1 and Bdf2 are at least partially redundant in function, their functions in the genome are geographically distinct. ..
- Zhang Z, Reese J. Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae. EMBO J. 2004;23:2246-57 pubmed..Our study has revealed a novel collaboration between two nucleosome-positioning activities in vivo, and suggests that disruption of nucleosome positioning is insufficient to cause a high level of transcription. ..
- Gavin I, Simpson R. Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J. 1997;16:6263-71 pubmed..We also show that a relatively high level of SUC2 transcription can coexist with positioned nucleosomes. ..
- Howe L, Kusch T, Muster N, Chaterji R, Yates J, Workman J. Yng1p modulates the activity of Sas3p as a component of the yeast NuA3 Hhistone acetyltransferase complex. Mol Cell Biol. 2002;22:5047-53 pubmed
- Zhang Q, Yoon Y, Yu Y, Parnell E, Garay J, Mwangi M, et al. Stochastic expression and epigenetic memory at the yeast HO promoter. Proc Natl Acad Sci U S A. 2013;110:14012-7 pubmed publisher..This memory is propagated in "cis" and reflects enhanced activator binding after a previous "on" cycle. We present evidence that the memory results from slow turnover of the histone acetylation marks...
- Utley R, Ikeda K, Grant P, Cote J, Steger D, Eberharter A, et al. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature. 1998;394:498-502 pubmed..Our results demonstrate the targeting of native HAT complexes by a transcription-activation domain to nucleosomes in order to activate transcription. ..
- Zhang Z, Wippo C, Wal M, Ward E, Korber P, Pugh B. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science. 2011;332:977-80 pubmed publisher..Thus, an active, nonstatistical nucleosome packing mechanism creates chromatin organizing centers at the 5' ends of genes where important regulatory elements reside. ..
- Yen K, Vinayachandran V, Pugh B. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 2013;154:1246-56 pubmed publisher..Our findings provide unifying concepts on how these two opposing chromatin remodeling complexes function selectively at the +1 nucleosome of nearly all genes...
- Döring K, Ahmed N, Riemer T, Suresh H, Vainshtein Y, Habich M, et al. Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding. Cell. 2017;170:298-311.e20 pubmed publisher..Ssb thus employs substrate-tailored dynamic nascent chain associations to coordinate co-translational protein folding, facilitate accelerated translation, and support membrane targeting of organellar proteins. ..
- Huisinga K, Pugh B. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biol. 2007;8:R46 pubmed..The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale. ..
- Sharma V, Tomar R, Dempsey A, Reese J. Histone deacetylases RPD3 and HOS2 regulate the transcriptional activation of DNA damage-inducible genes. Mol Cell Biol. 2007;27:3199-210 pubmed..Thus, reduced or unregulated constitutive histone H4 acetylation is detrimental to promoter activity, suggesting that HDAC-dependent mechanisms are in place to reset promoters to allow high levels of transcription. ..
- Zhang Z, Buchman A. Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Mol Cell Biol. 1997;17:5461-72 pubmed..These results suggest that DIS1 may contribute to making the silenced DNA template at HM loci more accessible during the mating-type switching process. ..
- Arellano Santoyo H, Geyer E, Stokasimov E, Chen G, Su X, Hancock W, et al. A Tubulin Binding Switch Underlies Kip3/Kinesin-8 Depolymerase Activity. Dev Cell. 2017;42:37-51.e8 pubmed publisher..Together, these findings elucidate a major regulatory mechanism controlling the size of cellular microtubule structures. ..
- Reese J. The control of elongation by the yeast Ccr4-not complex. Biochim Biophys Acta. 2013;1829:127-33 pubmed publisher..This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation. ..
- Yen K, Vinayachandran V, Batta K, Koerber R, Pugh B. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 2012;149:1461-73 pubmed publisher..Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays. ..
- Neely K, Workman J. The complexity of chromatin remodeling and its links to cancer. Biochim Biophys Acta. 2002;1603:19-29 pubmed..Their subunit composition and brief overview of their functional properties will be discussed. Also, current links between human chromatin-remodeling complexes and cell growth and cancer will be presented. ..
- Chitikila C, Huisinga K, Irvin J, Basehoar A, Pugh B. Interplay of TBP inhibitors in global transcriptional control. Mol Cell. 2002;10:871-82 pubmed..These findings reveal that transcriptional output is limited in part by a collaboration of different combinations of TBP inhibitory mechanisms. ..
- Zhang H, Reese J. Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3. Proc Natl Acad Sci U S A. 2007;104:8833-8 pubmed..Our results indicate that nucleosome placement plays a dominant role in repression and that the ability of the core promoter to position a nucleosome is a major determinant in TAF(II) dependency of genes in vivo. ..
- Chicca J, Auble D, Pugh B. Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1. Mol Cell Biol. 1998;18:1701-10 pubmed..Together, these findings suggest that human TAF-172 is the functional homolog of yeast Mot1 and uses the energy of ATP hydrolysis to remove TBP (but apparently not TBP-TAF complexes) from DNA. ..
- Psathas J, Zheng S, Tan S, Reese J. Set2-dependent K36 methylation is regulated by novel intratail interactions within H3. Mol Cell Biol. 2009;29:6413-26 pubmed publisher..We propose that Set2 activity is controlled by novel intratail interactions which can be influenced by modifications and changes to the structure of the H3 tail to control the dynamics and localization of methylation during elongation. ..
- Zhuang Z, Yoder B, Burgers P, Benkovic S. The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. Proc Natl Acad Sci U S A. 2006;103:2546-51 pubmed..The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm. ..