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David Shore

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David Shore was a Full Professor at the Department of Molecular Biology, University of Geneva from 1996-2020.

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2024

K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment.
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Mol Cell, ; 84 (12): 2337-2352.e9

2023

K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ).
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bioRxiv, ;
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.
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Genome Biol, ; 24 (1): 30

2022

Ribosome biogenesis and the cellular energy economy.
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Curr Biol, ; 32 (12): R611-R617

2021

Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals.
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Biochem Soc Trans, ; 49 (4): 1589-1599

2020

Mechanisms coordinating ribosomal protein gene transcription in response to stress.
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Nucleic Acids Res, ; 48 (20): 11408-11420
Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor.
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Mol Cell, ; 77 (3): 488-500.e9
Fork pausing complex engages topoisomerases at the replisome.
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Genes Dev, ; 34 (1-2): 87-98

2019

Opposing chromatin remodelers control transcription initiation frequency and start site selection.
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Nat Struct Mol Biol, ; 26 (8): 744-754
Rif1 S-acylation mediates DNA double-strand break repair at the inner nuclear membrane.
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Nat Commun, ; 10 (1): 2535
A ribosome assembly stress response regulates transcription to maintain proteome homeostasis.
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Elife, ; 8
Sfp1 regulates transcriptional networks driving cell growth and division through multiple promoter-binding modes.
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Genes Dev, ; 33 (5-6): 288-293

2018

General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation.
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Mol Cell, ; 72 (6): 955-969.e7
ChECing out Rif1 action in freely cycling cells.
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Curr Genet, ; 65 (2): 429-434
Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes.
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Genes Dev, ; 32 (17-18): 1252-1265
Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription.
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Mol Cell, ; 71 (1): 89-102.e5
Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration.
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Cell Rep, ; 23 (4): 983-992

2017

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends.
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Nat Struct Mol Biol, ; 24 (7): 588-595
Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler.
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Bioessays, ; 39 (5)
A Reply to "MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers," by Chereji et al.
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Mol Cell, ; 65 (3): 578-580
TFIID or not TFIID, a continuing transcriptional SAGA.
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EMBO J, ; 36 (3): 248-249

2016

A Molecular Titration System Coordinates Ribosomal Protein Gene Transcription with Ribosomal RNA Synthesis.
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Mol Cell, ; 64 (4): 720-733
Budding Yeast Rif1 Controls Genome Integrity by Inhibiting rDNA Replication.
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PLoS Genet, ; 12 (11): e1006414
Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.
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Cell Syst, ; 3 (3): 264-277.e10
Rif1: A Conserved Regulator of DNA Replication and Repair Hijacked by Telomeres in Yeasts.
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Front Genet, ; 7 : 45

2015

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast.
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Mol Cell, ; 60 (3): 422-434

2014

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.
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Genes Dev, ; 28 (15): 1695-1709
Rif1 controls DNA replication timing in yeast through the PP1 phosphatase Glc7.
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Cell Rep, ; 7 (1): 62-69

2013

A chemostat array enables the spatio-temporal analysis of the yeast proteome.
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Proc Natl Acad Sci U S A, ; 110 (39): 15842-15847
Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1.
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Curr Biol, ; 23 (17): 1638-1648
Rif1 and Rif2 shape telomere function and architecture through multivalent Rap1 interactions.
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Cell, ; 153 (6): 1340-1353

2012

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform.
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Proc Natl Acad Sci U S A, ; 109 (41): 16540-16545
The SUMO E3 ligase Siz2 exerts a locus-dependent effect on gene silencing in Saccharomyces cerevisiae.
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Eukaryot Cell, ; 11 (4): 452-462
Anticheckpoint pathways at telomeres in yeast.
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Nat Struct Mol Biol, ; 19 (3): 307-313
DNA-end capping by the budding yeast transcription factor and subtelomeric binding protein Tbf1.
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EMBO J, ; 31 (1): 138-149

2011

A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.
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Nat Struct Mol Biol, ; 18 (2): 213-221

2010

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.
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Mol Cell, ; 38 (4): 614-620

2009

Growth control and ribosome biogenesis.
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Curr Opin Cell Biol, ; 21 (6): 855-863
Telomere length regulation: coupling DNA end processing to feedback regulation of telomerase.
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EMBO J, ; 28 (16): 2309-2322
Sfp1 interaction with TORC1 and Mrs6 reveals feedback regulation on TOR signaling.
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Mol Cell, ; 33 (6): 704-716
Arsenic toxicity to Saccharomyces cerevisiae is a consequence of inhibition of the TORC1 kinase combined with a chronic stress response.
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Mol Biol Cell, ; 20 (3): 1048-1057

2008

Distinct roles for yeast Stn1 in telomere capping and telomerase inhibition.
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EMBO J, ; 27 (17): 2328-2339
How telomerase reaches its end: mechanism of telomerase regulation by the telomeric complex.
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Mol Cell, ; 31 (2): 153-165
Molecular biology. Refined view of the ends.
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Science, ; 320 (5881): 1301-1302

2007

Increased association of telomerase with short telomeres in yeast.
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Genes Dev, ; 21 (14): 1726-1730
Early replication of short telomeres in budding yeast.
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Cell, ; 128 (6): 1051-1062
DNA breaks are masked by multiple Rap1 binding in yeast: implications for telomere capping and telomerase regulation.
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Genes Dev, ; 21 (3): 292-302

2006

Fine-structure analysis of ribosomal protein gene transcription.
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Mol Cell Biol, ; 26 (13): 4853-4862

2005

Spontaneous rDNA copy number variation modulates Sir2 levels and epigenetic gene silencing.
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Genes Dev, ; 19 (10): 1199-1210

2004

Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1.
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Nature, ; 432 (7020): 1058-1061
Delivery of yeast telomerase to a DNA break depends on the recruitment functions of Cdc13 and Est1.
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Mol Cell, ; 16 (1): 139-146
Distinct DNA elements contribute to Rap1p affinity for its binding sites.
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J Mol Biol, ; 338 (5): 877-893
Pol12, the B subunit of DNA polymerase alpha, functions in both telomere capping and length regulation.
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Genes Dev, ; 18 (9): 992-1006

2002

Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8.
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Genetics, ; 162 (2): 633-645
In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation.
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J Mol Biol, ; 318 (2): 333-349

2001

Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast.
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Mol Cell Biol, ; 21 (23): 8082-8094
Telomere formation by rap1p binding site arrays reveals end-specific length regulation requirements and active telomeric recombination.
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Mol Cell Biol, ; 21 (23): 8117-8128
A role for Sds3p, a component of the Rpd3p/Sin3p deacetylase complex, in maintaining cellular integrity in Saccharomyces cerevisiae.
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Mol Genet Genomics, ; 265 (3): 560-568
Telomeric chromatin: replicating and wrapping up chromosome ends.
Curr Opin Genet Dev, ; 11 (2): 189-198

2000

Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity.
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J Biol Chem, ; 275 (52): 40961-40966
The Sir2 protein family: A novel deacetylase for gene silencing and more.
Proc Natl Acad Sci U S A, ; 97 (26): 14030-14032
Locus specificity determinants in the multifunctional yeast silencing protein Sir2.
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EMBO J, ; 19 (11): 2641-2651

1999

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.
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Nature, ; 402 (6760): 418-421
Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins.
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Curr Biol, ; 9 (19): 1123-1126

1998

1997

Telomerase and telomere-binding proteins: controlling the endgame.
Trends Biochem Sci, ; 22 (7): 233-235
Telomere length regulation: getting the measure of chromosome ends.
Biol Chem, ; 378 (7): 591-597
A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae.
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Genes Dev, ; 11 (6): 748-760
Telomeres. Different means to common ends.
Nature, ; 385 (6618): 676-677
A protein-counting mechanism for telomere length regulation in yeast.
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Science, ; 275 (5302): 986-990
Rap1p and telomere length regulation in yeast.
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Ciba Found Symp, ; 211 : 76-93; discussion 93-103

1996

Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae.
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Genetics, ; 144 (4): 1343-1353
SUM1-1, a dominant suppressor of SIR mutations in Saccharomyces cerevisiae, increases transcriptional silencing at telomeres and HM mating-type loci and decreases chromosome stability.
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Mol Cell Biol, ; 16 (8): 4281-4294
The means to bind the ends.
Nat Struct Biol, ; 3 (6): 491-493
Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein.
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Genes Dev, ; 10 (11): 1297-1309
Multimerization of Hsp42p, a novel heat shock protein of Saccharomyces cerevisiae, is dependent on a conserved carboxyl-terminal sequence.
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J Biol Chem, ; 271 (5): 2717-2723

1995

Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast.
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Genetics, ; 141 (4): 1253-1262
Suppressors of defective silencing in yeast: effects on transcriptional repression at the HMR locus, cell growth and telomere structure.
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Genetics, ; 141 (3): 873-888
Disturbance of normal cell cycle progression enhances the establishment of transcriptional silencing in Saccharomyces cerevisiae.
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Mol Cell Biol, ; 15 (7): 3608-3617
Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast.
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Genes Dev, ; 9 (3): 370-384

1994

Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1.
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Genes Dev, ; 8 (19): 2257-2269

1993

Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast.
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Cell, ; 75 (3): 531-541
Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae.
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Mol Cell Biol, ; 13 (7): 3919-3928
An essential yeast gene encoding a TTAGGG repeat-binding protein.
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Mol Cell Biol, ; 13 (2): 1306-1314

1992

A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation.
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Genes Dev, ; 6 (5): 801-814
Dissection of a carboxy-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing.
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Mol Cell Biol, ; 12 (3): 1209-1217

1991

Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length.
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Proc Natl Acad Sci U S A, ; 88 (17): 7749-7753
RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene.
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Mol Cell Biol, ; 11 (7): 3642-3651
RAP1 protein activates and silences transcription of mating-type genes in yeast.
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Genes Dev, ; 5 (4): 616-628

1990

Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length.
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Science, ; 250 (4980): 549-553

1987

Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements.
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Cell, ; 51 (5): 721-732
Transcriptional regulation in the yeast life cycle.
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Science, ; 237 (4819): 1162-1170
Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication.
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EMBO J, ; 6 (2): 461-467

1984

Characterization of two genes required for the position-effect control of yeast mating-type genes.
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EMBO J, ; 3 (12): 2817-2823

Former groups