Noncoding transcription influences the replication initiation program through chromatin regulation

Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast

(2017) Stefan Bresson et al.   MOLECULAR CELL

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

(2017) Carlo Baejen et al.   MOLECULAR CELL

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes

(2017) Nicole Uwimana et al.   NUCLEIC ACIDS RESEARCH

Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

(2017) Rob van Nues et al.   Nature Communications

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

(2017) Sina Wittmann et al.   Nature Communications

MCM: one ring to rule them all

(2016) Tom D Deegan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase

(2016) Jared M. Peace et al.   GENOME RESEARCH

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

(2016) Jairo Rodriguez et al.   GENOME RESEARCH

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers

(2016) Benoit Miotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly

(2015) Jason A. Belsky et al.   GENES & DEVELOPMENT

Replication timing is regulated by the number of MCMs loaded at origins

(2015) Shankar P. Das et al.   GENOME RESEARCH

Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA

(2015) Julien Gros et al.   MOLECULAR CELL

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

(2015) Slawomir Kubik et al.   MOLECULAR CELL

High-Resolution Chromatin Dynamics during a Yeast Stress Response

(2015) Assaf Weiner et al.   MOLECULAR CELL

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

(2015) Christophe Malabat et al.   eLife

Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae

(2014) Ignacio Soriano et al.   BMC GENOMICS

Elucidation of the DNA End-Replication Problem in Saccharomyces cerevisiae

(2014) Julien Soudet et al.   MOLECULAR CELL

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

(2014) Agnieszka Tudek et al.   MOLECULAR CELL

The Histone Deacetylases Sir2 and Rpd3 Act on Ribosomal DNA to Control the Replication Program in Budding Yeast

(2014) Kazumasa Yoshida 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

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

(2014) Fabrice P. A. David et al.   PLoS One

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

Location, location, location: it's all in the timing for replication origins

(2013) O. M. Aparicio   GENES & DEVELOPMENT

Time to Be Versatile: Regulation of the Replication Timing Program in Budding Yeast

(2013) Kazumasa Yoshida et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantitative, Genome-Wide Analysis of Eukaryotic Replication Initiation and Termination

(2013) Sean R. McGuffee et al.   MOLECULAR CELL

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

(2013) Manuele Castelnuovo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAP-II Molecules Participate in the Anchoring of the ORC to rDNA Replication Origins

(2013) Maria D. Mayan   PLoS One

High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

(2013) Michelle Hawkins et al.   Cell Reports

A Link between ORC-Origin Binding Mechanisms and Origin Activation Time Revealed in Budding Yeast

(2013) Timothy Hoggard et al.   PLoS Genetics

Cell-cycle regulated transcription associates with DNA replication timing in yeast and human

(2013) Hunter B Fraser   GENOME BIOLOGY

Forkhead Transcription Factors Establish Origin Timing and Long-Range Clustering in S. cerevisiae

(2012) Simon R.V. Knott et al.   CELL

Chromatin-dependent and -independent regulation of DNA replication origin activation in budding yeast

(2012) Marko Lõoke et al.   EMBO REPORTS

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

(2012) G. I. Dellino et al.   GENOME RESEARCH

Separation of DNA Replication from the Assembly of Break-Competent Meiotic Chromosomes

(2012) Hannah G. Blitzblau et al.   PLoS Genetics

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Conserved nucleosome positioning defines replication origins

(2010) M. L. Eaton et al.   GENES & DEVELOPMENT

Relicensing of Transcriptionally Inactivated Replication Origins in Budding Yeast

(2010) Marko Lõoke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing

(2010) Scott Cheng-Hsin Yang et al.   Molecular Systems Biology

Dynamic changes in histone acetylation regulate origins of DNA replication

(2010) Ashwin Unnikrishnan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

H3 K36 Methylation Helps Determine the Timing of Cdc45 Association with Replication Origins

(2009) Fiona Pryde et al.   PLoS One

Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

(2009) Joana Sequeira-Mendes et al.   PLoS Genetics

The Anchor-Away Technique: Rapid, Conditional Establishment of Yeast Mutant Phenotypes

(2008) Hirohito Haruki et al.   MOLECULAR CELL

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

DNA Combing Reveals Intrinsic Temporal Disorder in the Replication of Yeast Chromosome VI

(2007) Daniel M. Czajkowsky et al.   JOURNAL OF MOLECULAR BIOLOGY