Environmental change drives accelerated adaptation through stimulated copy number variation

Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains

(2017) Jacob Steenwyk et al.   G3-Genes Genomes Genetics

Transcription leads to pervasive replisome instability in bacteria

(2017) Sarah M Mangiameli et al.   eLife

Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

(2016) Pei-Chi Wei et al.   CELL

Copy number variations of genes involved in stress responses reflect the redox state and DNA damage in brewing yeasts

(2016) Jagoda Adamczyk et al.   CELL STRESS & CHAPERONES

The nature of mutations induced by replication–transcription collisions

(2016) T. Sabari Sankar et al.   NATURE

Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells

(2016) Bjoern Schwer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

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

Extrachromosomal circular DNA is common in yeast

(2015) Henrik D. Møller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyper-Acetylation of Histone H3K56 Limits Break-Induced Replication by Inhibiting Extensive Repair Synthesis

(2015) Jun Che et al.   PLoS Genetics

Complex correlations: replication timing and mutational landscapes during cancer and genome evolution

(2014) Jiao Sima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcription factor regulation and chromosome dynamics during pseudohyphal growth

(2014) David Mayhew et al.   MOLECULAR BIOLOGY OF THE CELL

Structures of Naturally Evolved CUP1 Tandem Arrays in Yeast Indicate That These Arrays Are Generated by Unequal Nonhomologous Recombination

(2014) Ying Zhao et al.   G3-Genes Genomes Genetics

Metabolic Respiration Induces AMPK- and Ire1p-Dependent Activation of the p38-Type HOG MAPK Pathway

(2014) Hema Adhikari et al.   PLoS Genetics

Endogenous RNA interference is driven by copy number

(2014) Cristina Cruz et al.   eLife

Causes of Genome Instability

(2013) Andrés Aguilera et al.   Annual Review of Genetics

A small molecule inhibitor of fungal histone acetyltransferase Rtt109

(2013) Jessica Lopes da Rosa et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Replication Stress-Induced Genome Instability: The Dark Side of Replication Maintenance by Homologous Recombination

(2013) Antony M. Carr et al.   JOURNAL OF MOLECULAR BIOLOGY

The Yeast Snt2 Protein Coordinates the Transcriptional Response to Hydrogen Peroxide-Mediated Oxidative Stress

(2013) L. A. Baker et al.   MOLECULAR AND CELLULAR BIOLOGY

Accelerated gene evolution through replication–transcription conflicts

(2013) Sandip Paul et al.   NATURE

Rescuing Stalled or Damaged Replication Forks

(2013) J. T. P. Yeeles et al.   Cold Spring Harbor Perspectives in Biology

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

(2013) Satoru Ide et al.   PLoS Genetics

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

(2013) Erika Shor et al.   PLoS Genetics

Mechanisms for recurrent and complex human genomic rearrangements

(2012) Pengfei Liu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

(2012) B. Dunn et al.   GENOME RESEARCH

Amplification of the CUP1 gene is associated with evolution of copper tolerance in Saccharomyces cerevisiae

(2012) G. M. Adamo et al.   MICROBIOLOGY-SGM

Recombination-restarted replication makes inverted chromosome fusions at inverted repeats

(2012) Ken’Ichi Mizuno et al.   NATURE

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Histone H3-K56 acetylation is important for genomic stability in mammals

(2011) Jian Yuan et al.   CELL CYCLE

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery

(2011) Jonathan Houseley et al.   NUCLEIC ACIDS RESEARCH

Amplification of the Driving Oncogene, KRAS or BRAF, Underpins Acquired Resistance to MEK1/2 Inhibitors in Colorectal Cancer Cells

(2011) A. S. Little et al.   Science Signaling

Functional consequences of bidirectional promoters

(2011) Wu Wei et al.   TRENDS IN GENETICS

Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence

(2011) Silvère M. van der Maarel et al.   TRENDS IN MOLECULAR MEDICINE

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

The Rtt109 histone acetyltransferase facilitates error-free replication to prevent CAG/CTG repeat contractions

(2010) Jiahui H. Yang et al.   DNA REPAIR

Chemogenomic profiling of the cellular effects associated with histone H3 acetylation impairment by a quinoline-derived compound

(2010) Roberta Ruotolo et al.   GENOMICS

Homologous Recombination Restarts Blocked Replication Forks at the Expense of Genome Rearrangements by Template Exchange

(2010) Sarah Lambert et al.   MOLECULAR CELL

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

(2010)   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX

(2010) Rachel K Szilard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

(2010) D. Gresham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BRAF Gene Amplification Can Promote Acquired Resistance to MEK Inhibitors in Cancer Cells Harboring the BRAF V600E Mutation

(2010) R. B. Corcoran et al.   Science Signaling

The Mother Enrichment Program: A Genetic System for Facile Replicative Life Span Analysis in Saccharomyces cerevisiae

(2009) D. L. Lindstrom et al.   GENETICS

Aberrant Double-Strand Break Repair Resulting in Half Crossovers in Mutants Defective for Rad51 or the DNA Polymerase   Complex

(2009) C. E. Smith et al.   MOLECULAR AND CELLULAR BIOLOGY

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces cerevisiae

(2009) Anna Azvolinsky et al.   MOLECULAR CELL

CBP/p300-mediated acetylation of histone H3 on lysine 56

(2009) Chandrima Das et al.   NATURE

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

The Biochemistry of Somatic Hypermutation

(2008) Jonathan U. Peled et al.   Annual Review of Immunology

Mechanism and Regulation of Class Switch Recombination

(2008) Janet Stavnezer et al.   Annual Review of Immunology

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

Defective Break-Induced Replication Leads to Half-Crossovers in Saccharomyces cerevisiae

(2008) A. Deem et al.   GENETICS

Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage

(2008) I. Celic et al.   GENETICS

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

(2008) Jonathan Houseley et al.   MOLECULAR CELL

Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms

(2008) Celia Payen et al.   PLoS Genetics