Gene repression in S. cerevisiae—looking beyond Sir-dependent gene silencing

Conserved chromosomal functions of RNA interference

(2020) Michael J. Gutbrod et al.   NATURE REVIEWS GENETICS

The acetyltransferase Eco1 elicits cohesin dimerization during S phase

(2020) Di Shi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions

(2020) Julia V. DiFiore et al.   Cell Reports

A SIR-independent role for cohesin in subtelomeric silencing and organization

(2019) Deepash Kothiwal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The copper-sensing transcription factor Mac1, the histone deacetylase Hst1, and nicotinic acid regulate de novo NAD+ biosynthesis in budding yeast

(2019) Christol James Theoga Raj et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to the HO Promoter in Saccharomyces cerevisiae

(2019) Emily J. Parnell et al.   GENETICS

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

(2019) Jessica L. Feldman et al.   Cell Reports

Dysfunctional CAF-I reveals its role in cell cycle progression and differential regulation of gene silencing

(2019) Hollie Rowlands et al.   CELL CYCLE

Nut1/Hos1 and Sas2/Rpd3 control the H3 acetylation of two different sets of osmotic stress-induced genes

(2019) María E. Pérez-Martínez et al.   Epigenetics

Histone chaperones and the Rrm3p helicase regulate flocculation in S. cerevisiae

(2019) Hollie Rowlands et al.   Epigenetics & Chromatin

Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast

(2019) So Dam Ha et al.   Nature Communications

Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

(2018) Rahul Kumar Jangid et al.   BMC GENOMICS

Large-scale profiling of noncoding RNA function in yeast

(2018) Steven Parker et al.   PLoS Genetics

Impaired cohesion and homologous recombination during replicative aging in budding yeast

(2018) Sangita Pal et al.   Science Advances

Set4 is a chromatin-associated protein, promotes survival during oxidative stress, and regulates stress response genes in yeast

(2018) Khoa Tran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Centromeres License the Mitotic Condensation of Yeast Chromosome Arms

(2018) Tom Kruitwagen et al.   CELL

Histone modifications and the DNA double-strand break response

(2018) Hieu T. Van et al.   CELL CYCLE

SET domains and stress: uncovering new functions for yeast Set4

(2018) Khoa Tran et al.   CURRENT GENETICS

HST1 increases replicative lifespan of a sir2Δ mutant in the absence of PDE2 in Saccharomyces cerevisiae

(2017) Woo Kyu Kang et al.   JOURNAL OF MICROBIOLOGY

Choose Your Own Adventure: The Role of Histone Modifications in Yeast Cell Fate

(2017) Deepika Jaiswal et al.   JOURNAL OF MOLECULAR BIOLOGY

Smc3 Deacetylation by Hos1 Facilitates Efficient Dissolution of Sister Chromatid Cohesion during Early Anaphase

(2017) Shuyu Li et al.   MOLECULAR CELL

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sas3 and Ada2(Gcn5)-dependent histone H3 acetylation is required for transcription elongation at the de-repressedFLO1gene

(2017) Michael Church et al.   NUCLEIC ACIDS RESEARCH

H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity

(2017) Stephen L. McDaniel et al.   Cell Reports

Repression of Middle Sporulation Genes in Saccharomyces cerevisiae by the Sum1-Rfm1-Hst1 Complex Is Maintained by Set1 and H3K4 Methylation

(2017) Deepika Jaiswal et al.   G3-Genes Genomes Genetics

The long non-coding RNA world in yeasts

(2016) Akira Yamashita et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Epigenetic Mechanisms of Longevity and Aging

(2016) Payel Sen et al.   CELL

The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

(2016) Meagan Jezek et al.   Epigenetics

Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation

(2016) Deborah M. Thurtle-Schmidt et al.   GENETICS

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

(2016) Marc R. Gartenberg et al.   GENETICS

Selective suppression of antisense transcription by Set2-mediated H3K36 methylation

(2016) Swaminathan Venkatesh et al.   Nature Communications

Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation

(2016) Deborah M. Thurtle-Schmidt et al.   GENETICS

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

(2016) Marc R. Gartenberg et al.   GENETICS

Epigenetics and aging

(2016) S. Pal et al.   Science Advances

Emerging roles of lysine methylation on non-histone proteins

(2015) Xi Zhang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

(2015) Payel Sen et al.   GENES & DEVELOPMENT

Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry

(2015) Jeffrey N. McKnight et al.   MOLECULAR CELL

Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification

(2015) Aurélie Lardenois et al.   MOLECULAR GENETICS AND GENOMICS

Regulation of ribosomal DNA amplification by the TOR pathway

(2015) Carmen V. Jack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

(2015) Anne E Dodson et al.   eLife

SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae

(2015) Ritu Gupta et al.   PLoS One

The yeast Cyc8–Tup1 complex cooperates with Hda1p and Rpd3p histone deacetylases to robustly repress transcription of the subtelomeric FLO1 gene

(2014) Alastair B. Fleming et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons

(2014) Glòria Mas Martín et al.   Epigenetics

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

(2014) Michael Downey et al.   MOLECULAR & CELLULAR PROTEOMICS

A lysine deacetylase Hos3 is targeted to the bud neck and involved in the spindle position checkpoint

(2014) Mengqiao Wang et al.   MOLECULAR BIOLOGY OF THE CELL

NuA4 Initiates Dynamic Histone H4 Acetylation to Promote High-Fidelity Sister Chromatid Recombination at Postreplication Gaps

(2014) Nealia C.M. House et al.   MOLECULAR CELL

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

(2014) Manuele Castelnuovo et al.   NUCLEIC ACIDS RESEARCH

A Cascade of Histone Modifications Induces Chromatin Condensation in Mitosis

(2014) Bryan J. Wilkins et al.   SCIENCE

Erasers of Histone Acetylation: The Histone Deacetylase Enzymes

(2014) E. Seto et al.   Cold Spring Harbor Perspectives in Biology

Gcn5 and Sirtuins Regulate Acetylation of the Ribosomal Protein Transcription Factor Ifh1

(2013) Michael Downey et al.   CURRENT BIOLOGY

The Roles of the Catalytic and Noncatalytic Activities of Rpd3L and Rpd3S in the Regulation of Gene Transcription in Yeast

(2013) Daniella Yeheskely-Hayon et al.   PLoS One

Stepwise histone modifications are mediated by multiple enzymes that rapidly associate with nascent DNA during replication

(2013) Svetlana Petruk et al.   Nature Communications

A Reversible Histone H3 Acetylation Cooperates with Mismatch Repair and Replicative Polymerases in Maintaining Genome Stability

(2013) Lyudmila Y. Kadyrova et al.   PLoS Genetics

Rtt109 Prevents Hyper-Amplification of Ribosomal RNA Genes through Histone Modification in Budding Yeast

(2013) Satoru Ide et al.   PLoS Genetics

Xbp1 Directs Global Repression of Budding Yeast Transcription during the Transition to Quiescence and Is Important for the Longevity and Reversibility of the Quiescent State

(2013) Shawna Miles et al.   PLoS Genetics

Genome-wide analysis of functional sirtuin chromatin targets in yeast

(2013) Mingguang Li et al.   GENOME BIOLOGY

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast

(2012) Folkert J. van Werven et al.   CELL

TrxG and PcG Proteins but Not Methylated Histones Remain Associated with DNA through Replication

(2012) Svetlana Petruk et al.   CELL

Nutritional Control of Growth and Development in Yeast

(2012) J. R. Broach   GENETICS

The histone deacetylase Hos2 forms an Hsp42-dependent cytoplasmic granule in quiescent yeast cells

(2012) I-Chun Liu et al.   MOLECULAR BIOLOGY OF THE CELL

Single-Cell Analysis Reveals that Noncoding RNAs Contribute to Clonal Heterogeneity by Modulating Transcription Factor Recruitment

(2012) Stacie L. Bumgarner et al.   MOLECULAR CELL

Multiple histone deacetylases are recruited by corepressor Sin3 and contribute to gene repression mediated by Opi1 regulator of phospholipid biosynthesis in the yeast Saccharomyces cerevisiae

(2012) Mathias Grigat et al.   MOLECULAR GENETICS AND GENOMICS

Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress

(2012) Johnny M. Tkach et al.   NATURE CELL BIOLOGY

Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses

(2012) Erin M Green et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

(2012) Thanasis Margaritis et al.   PLoS Genetics

The Rpd3 Core Complex Is a Chromatin Stabilization Module

(2011) Xiao-Fen Chen et al.   CURRENT BIOLOGY

The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein

(2011) K. H. Wong et al.   GENES & DEVELOPMENT

RNA Polymerase II Carboxyl-terminal Domain Phosphorylation Regulates Protein Stability of the Set2 Methyltransferase and Histone H3 Di- and Trimethylation at Lysine 36

(2011) Stephen M. Fuchs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

(2011) Benoit Guillemette et al.   PLoS Genetics

Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2

(2010) J.-H. Kim et al.   GENES & DEVELOPMENT

Thiamine Biosynthesis in Saccharomyces cerevisiae Is Regulated by the NAD+-Dependent Histone Deacetylase Hst1

(2010) M. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

Elevated Histone Expression Promotes Life Span Extension

(2010) Jason Feser et al.   MOLECULAR CELL

The Rpd3L HDAC complex is essential for the heat stress response in yeast

(2010) Clàudia Ruiz-Roig et al.   MOLECULAR MICROBIOLOGY

Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate

(2010) S. Ehrentraut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dimethylation of H3K4 by Set1 Recruits the Set3 Histone Deacetylase Complex to 5′ Transcribed Regions

(2009) TaeSoo Kim et al.   CELL

The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters

(2009) Shinya Takahata et al.   EMBO JOURNAL

H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation

(2009) Marina Pinskaya et al.   EMBO JOURNAL

Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae

(2009) S. R.V. Knott et al.   GENES & DEVELOPMENT

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

(2009) J. Camblong et al.   GENES & DEVELOPMENT

Histone H4 lysine 16 acetylation regulates cellular lifespan

(2009) Weiwei Dang et al.   NATURE

Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation

(2009) Jing Zhou et al.   NUCLEIC ACIDS RESEARCH

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

(2009) S. L. Bumgarner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hos2p/Set3p Deacetylase Complex Signals Secretory Stress through the Mpk1p Cell Integrity Pathway

(2008) T. J. Cohen et al.   EUKARYOTIC CELL

A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae

(2008) J. Berretta et al.   GENES & DEVELOPMENT

Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage

(2008) I. Celic et al.   GENETICS

HST3/HST4-dependent Deacetylation of Lysine 56 of Histone H3 in Silent Chromatin

(2008) Bo Yang et al.   MOLECULAR BIOLOGY OF THE CELL

A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster

(2008) Jonathan Houseley et al.   MOLECULAR CELL