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Hongfang Qiu, Răzvan V Chereji, Cuihua Hu, Hope A Cole, Yashpal Rawal, David J Clark, Alan G Hinnebusch
Chaperones, nucleosome remodeling complexes, and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these cofactors function ubiquitously, as well as the impact of nucleosome eviction on transcription genome-wide, is poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple cofactors to address these issues for about 200 genes belonging to the Gcn4 transcriptome, of which about 70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation...
February 2016: Genome Research
Laura M Lombardi, Matthew D Davis, Jasper Rine
The extent of chromatin compaction is a fundamental driver of nuclear metabolism . Yta7 is a chromatin-associated AAA-ATPase, the human ortholog of which, ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. Yta7 directly binds histone H3, and bulk chromatin exhibits increased nucleosomal density in yta7Δ mutants. The suppression of yta7Δ mutant growth and transcriptional phenotypes in budding yeast by decreased dosage of histones H3 and H4 indicates the acute sensitivity of cells to deviations in nucleosome spacing...
January 2015: Genetics
Matteo Cattaneo, Yuichi Morozumi, Daniel Perazza, Fayçal Boussouar, Mahya Jamshidikia, Sophie Rousseaux, André Verdel, Saadi Khochbin
ATAD2, a remarkably conserved, yet poorly characterized factor is found upregulated and associated with poor prognosis in a variety of independent cancers in human. Studies conducted on the yeast Saccharomyces cerevisiae ATAD2 homologue, Yta7, are now indicating that the members of this family may primarily be regulators of chromatin dynamics and that their action on gene expression could only be one facet of their general activity. In this review, we present an overview of the literature on Yta7 and discuss the possibility of translating these findings into other organisms to further define the involvement of ATAD2 and other members of its family in regulating chromatin structure and function both in normal and pathological situations...
December 31, 2014: Molecules and Cells
Rachel M Zunder, Jasper Rine
In Saccharomyces cerevisiae, the histone chaperone Rtt106 binds newly synthesized histone proteins and mediates their delivery into chromatin during transcription, replication, and silencing. Rtt106 is also recruited to histone gene regulatory regions by the HIR histone chaperone complex to ensure S-phase-specific expression. Here we showed that this Rtt106:HIR complex included Asf1 and histone proteins. Mutations in Rtt106 that reduced histone binding reduced Rtt106 enrichment at histone genes, leading to their increased transcription...
November 2012: Molecular and Cellular Biology
Christoph F Kurat, Jean-Philippe Lambert, Dewald van Dyk, Kyle Tsui, Harm van Bakel, Supipi Kaluarachchi, Helena Friesen, Pinay Kainth, Corey Nislow, Daniel Figeys, Jeffrey Fillingham, Brenda J Andrews
The cell cycle-regulated expression of core histone genes is required for DNA replication and proper cell cycle progression in eukaryotic cells. Although some factors involved in histone gene transcription are known, the molecular mechanisms that ensure proper induction of histone gene expression during S phase remain enigmatic. Here we demonstrate that S-phase transcription of the model histone gene HTA1 in yeast is regulated by a novel attach-release mechanism involving phosphorylation of the conserved chromatin boundary protein Yta7 by both cyclin-dependent kinase 1 (Cdk1) and casein kinase 2 (CK2)...
December 1, 2011: Genes & Development
Laura M Lombardi, Aisha Ellahi, Jasper Rine
Yta7 is a highly conserved bromodomain-containing protein with AAA-ATPase homology originally implicated in heterochromatin boundary function in Saccharomyces cerevisiae. Although increased activity of the human ortholog has been implicated in malignant breast tumors, Yta7's precise mode of action is unknown. Transcriptional analysis in yeast cells revealed a role for Yta7 and its ATPase function in gene induction, including galactose- and sporulation-induced transcription. This requirement was direct and activating, because Yta7 associated with the GAL gene cluster only upon transcriptional induction...
December 6, 2011: Proceedings of the National Academy of Sciences of the United States of America
Jeffrey Fillingham, Pinay Kainth, Jean-Philippe Lambert, Harm van Bakel, Kyle Tsui, Lourdes Peña-Castillo, Corey Nislow, Daniel Figeys, Timothy R Hughes, Jack Greenblatt, Brenda J Andrews
We describe a fluorescent reporter system that exploits the functional genomic tools available in budding yeast to systematically assess consequences of genetic perturbations on gene expression. We used our Reporter-Synthetic Genetic Array (R-SGA) method to screen for regulators of core histone gene expression. We discovered that the histone chaperone Rtt106 functions in a pathway with two other chaperones, Asf1 and the HIR complex, to create a repressive chromatin structure at core histone promoters. We found that activation of histone (HTA1) gene expression involves both relief of Rtt106-mediated repression by the activity of the histone acetyltransferase Rtt109 and restriction of Rtt106 to the promoter region by the bromodomain-containing protein Yta7...
August 14, 2009: Molecular Cell
Angeline Gradolatto, Sherri K Smart, Stephanie Byrum, Lauren P Blair, Richard S Rogers, Elizabeth A Kolar, Heather Lavender, Signe K Larson, John D Aitchison, Sean D Taverna, Alan J Tackett
Saccharomyces cerevisiae Yta7 is a barrier active protein that modulates transcriptional states at the silent mating locus, HMR. Additionally, Yta7 regulates histone gene transcription and has overlapping functions with known histone chaperones. This study focused on deciphering the functional role of the noncanonical Yta7 bromodomain. By use of genetic and epistasis analyses, the Yta7 bromodomain was shown to be necessary for barrier activity at HMR and to have overlapping functions with histone regulators (Asf1 and Spt16)...
September 2009: Molecular and Cellular Biology
Klaudia Kuranda, Kariona Grabinska, Thierry Berges, Francis Karst, Veronique Leberre, Serguei Sokol, Jean François, Grazyna Palamarczyk
The isoprenoid pathway in yeasts is important not only for sterol biosynthesis but also for the production of nonsterol molecules, deriving from farnesyl diphosphate (FPP), implicated in N-glycosylation and biosynthesis of heme and ubiquinones. FPP formed from mevalonate in a reaction catalyzed by FPP synthase (Erg20p). In order to investigate the regulation of Erg20p in Saccharomyces cerevisiae, we searched for its protein partners using a two-hybrid screen, and identified five interacting proteins, among them Yta7p...
May 2009: FEMS Yeast Research
Angeline Gradolatto, Richard S Rogers, Heather Lavender, Sean D Taverna, C David Allis, John D Aitchison, Alan J Tackett
The Saccharomyces cerevisiae Yta7 protein is a component of a nucleosome bound protein complex that maintains distinct transcriptional zones of chromatin. We previously found that one protein copurifying with Yta7 is the yFACT member Spt16. Epistasis analyses revealed a link between Yta7, Spt16, and other previously identified members of the histone regulatory pathway. In concurrence, Yta7 was found to regulate histone gene transcription in a cell-cycle-dependent manner. Association at the histone gene loci appeared to occur through binding of the bromodomain-like region of Yta7 with the N-terminal tail of histone H3...
May 2008: Genetics
Rong-Jeng Tseng, Kristin R Armstrong, Xiaodong Wang, Helen M Chamberlin
In many organisms, repetitive DNA serves as a trigger for gene silencing. However, some gene expression is observed from repetitive genomic regions such as heterochromatin, suggesting mechanisms exist to modulate the silencing effects. From a genetic screen in C. elegans, we have identified mutations in two genes important for expression of repetitive sequences: lex-1 and tam-1. Here we show that lex-1 encodes a protein containing an ATPase domain and a bromodomain. LEX-1 is similar to the yeast Yta7 protein, which maintains boundaries between silenced and active chromatin...
November 2007: Molecular Genetics and Genomics: MGG
Nithya Jambunathan, Adam W Martinez, Elizabeth C Robert, Nneamaka B Agochukwu, Megan E Ibos, Sandra L Dugas, David Donze
The transfer RNA gene downstream from the HMR locus in S. cerevisiae functions as part of a boundary (barrier) element that restricts the spread of heterochromatic gene silencing into the downstream region of chromosome III. A genetic screen for identifying additional genes that, when mutated, allow inappropriate spreading of silencing from HMR through the tRNA gene was performed. YTA7, a gene containing bromodomain and ATPase homologies, was identified multiple times. Previously, others had shown that the bromodomain protein Bdf1p functions to restrict silencing at yeast euchromatin-heterochromatin boundaries; therefore we deleted nonessential bromodomain-containing genes to test their effects on heterochromatin spreading...
November 2005: Genetics
Alan J Tackett, David J Dilworth, Megan J Davey, Michael O'Donnell, John D Aitchison, Michael P Rout, Brian T Chait
We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin. These assemblies contain characteristic stretches of DNA that flank particular regions of silent chromatin, as well as five distinctively modified histones and a set of protein complexes. The complexes consist of at least 15 chromatin-associated proteins, including DNA pol epsilon, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase...
April 11, 2005: Journal of Cell Biology
Kariona Grabińska, Grazyna Palamarczyk
Dolichol, an isoprenoid lipid, known mainly for its function in protein glycosylation, is synthesised in the mevalonate pathway. The pathway is highly regulated, on multiple levels, by sterol and non-sterol derivatives of mevalonic acid. Farnesyl diphosphate (FPP) and/or FPP-derived molecules have been identified as the main non-sterol compounds regulating degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, one of the regulatory enzymes in the mevalonate pathway. In the present review we concentrate on the effect of overexpression of farnesyl diphosphate synthase on dolichol biosynthesis in yeast...
August 2002: FEMS Yeast Research
M L Agostoni Carbone, G Lucchini, P Melchioretto, V Nardese, M Vanoni, L Panzeri
In the framework of the EU programme for systematic sequencing of the Saccharomyces cervisiae genome we determined the sequence of a 9359 bp fragment of the right arm of chromosome VII. Five open reading frames (ORFs) of at least 300 nucleotides were found in this region. YGR267c encodes a protein with significant similarity to the enzyme GTP-cyclohydrolase I, that controls the first step in the biosynthetic pathway leading to various pterins and shows a high degree of sequence conservation from bacteria to mammals...
April 30, 1998: Yeast
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