End of the Beginning: Elongation and Termination Features of Alternative Modes of Chromosomal Replication Initiation in Bacteria

Chromosome replication origins: Do we really need them?

(2014) Bénédicte Michel et al.   BIOESSAYS

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

ATR checkpoint kinase and CRL1 TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks

(2014) J.-S. Im et al.   GENES & DEVELOPMENT

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer

(2014) B. Youngren et al.   GENES & DEVELOPMENT

BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks

(2014) Nicholas A. Willis et al.   NATURE

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

(2014) Vaibhav Bhatia et al.   NATURE

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Cdc48 and a ubiquitin ligase drive disassembly of the CMG helicase at the end of DNA replication

(2014) Marija Maric et al.   SCIENCE

Cancer Suppression by the Chromosome Custodians, BRCA1 and BRCA2

(2014) A. R. Venkitaraman   SCIENCE

Polyubiquitylation drives replisome disassembly at the termination of DNA replication

(2014) Sara Priego Moreno et al.   SCIENCE

Mechanisms of genome instability induced by RNA-processing defects

(2014) Yujia A. Chan et al.   TRENDS IN GENETICS

Transcription and Recombination: When RNA Meets DNA

(2014) A. Aguilera et al.   Cold Spring Harbor Perspectives in Biology

End Resection at Double-Strand Breaks: Mechanism and Regulation

(2014) L. S. Symington   Cold Spring Harbor Perspectives in Biology

Out of Balance: R-loops in Human Disease

(2014) Matthias Groh et al.   PLoS Genetics

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

(2014) Yujia A. Chan et al.   PLoS Genetics

Roles of Type 1A Topoisomerases in Genome Maintenance in Escherichia coli

(2014) Valentine Usongo et al.   PLoS Genetics

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

(2014) Aziz El Hage et al.   PLoS Genetics

End-resection at DNA double-strand breaks in the three domains of life: Figure 1

(2013) John K. Blackwood et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

DNA replication and homologous recombination factors: acting together to maintain genome stability

(2013) Antoine Aze et al.   CHROMOSOMA

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 Intertwined Roles of Transcription and Repair Proteins

(2013) Yick W. Fong et al.   MOLECULAR CELL

Replication of theEscherichia colichromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics

(2013) Nkabuije Z. Maduike et al.   MOLECULAR MICROBIOLOGY

Accelerated growth in the absence of DNA replication origins

(2013) Michelle Hawkins et al.   NATURE

Avoiding chromosome pathology when replication forks collide

(2013) Christian J. Rudolph et al.   NATURE

Transcription-replication encounters, consequences and genomic instability

(2013) Anne Helmrich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Principles and Concepts of DNA Replication in Bacteria, Archaea, and Eukarya

(2013) M. O'Donnell et al.   Cold Spring Harbor Perspectives in Biology

Archaeology of Eukaryotic DNA Replication

(2013) K. S. Makarova et al.   Cold Spring Harbor Perspectives in Biology

Repair of Strand Breaks by Homologous Recombination

(2013) M. Jasin et al.   Cold Spring Harbor Perspectives in Biology

Rescuing Stalled or Damaged Replication Forks

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

DNA Replication Origins

(2013) A. C. Leonard et al.   Cold Spring Harbor Perspectives in Biology

Regulating DNA Replication in Bacteria

(2013) K. Skarstad et al.   Cold Spring Harbor Perspectives in Biology

R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli

(2013) Hallie Wimberly et al.   Nature Communications

Pre-mRNA processing factors meet the DNA damage response

(2013) Alessandra Montecucco et al.   Frontiers in Genetics

Chromosome Replication and Segregation in Bacteria

(2012) Rodrigo Reyes-Lamothe et al.   Annual Review of Genetics

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability

(2012) R. Steinacher et al.   GENES & DEVELOPMENT

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

(2012) J. M. Peters et al.   GENES & DEVELOPMENT

Disintegration of Nascent Replication Bubbles during Thymine Starvation Triggers RecA- and RecBCD-dependent Replication Origin Destruction

(2012) Kawai J. Kuong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Preventing Replication Stress to Maintain Genome Stability: Resolving Conflicts between Replication and Transcription

(2012) Rodrigo Bermejo et al.   MOLECULAR CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

The conflict between DNA replication and transcription

(2012) Peter McGlynn et al.   MOLECULAR MICROBIOLOGY

Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB

(2012) Dale B. Wigley   NATURE REVIEWS MICROBIOLOGY

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

(2012) Feng Gao et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Holliday Junction Resolving Enzyme Encoded by the Bacillus subtilis Bacteriophage SPP1

(2012) Lisa Zecchi et al.   PLoS One

Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli

(2012) J. Krishna Leela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

Replication Fork Reversal after Replication–Transcription Collision

(2012) Anne L. De Septenville et al.   PLoS Genetics

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

DNA end resection—Unraveling the tail

(2011) Eleni P. Mimitou et al.   DNA REPAIR

The effect of the intra-S-phase checkpoint on origins of replication in human cells

(2011) Neerja Karnani et al.   GENES & DEVELOPMENT

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

Replication Forks Stalled at Ultraviolet Lesions Are Rescued via RecA and RuvABC Protein-catalyzed Disintegration inEscherichia coli

(2011) Sharik R. Khan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes

(2011) Anne Helmrich et al.   MOLECULAR CELL

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability

(2011) Lamia Wahba et al.   MOLECULAR CELL

Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

(2011) Hannah E. Mischo et al.   MOLECULAR CELL

Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination

(2011) K. Anupama et al.   MOLECULAR MICROBIOLOGY

Co-directional replication–transcription conflicts lead to replication restart

(2011) Houra Merrikh et al.   NATURE

How dormant origins promote complete genome replication

(2011) J. Julian Blow et al.   TRENDS IN BIOCHEMICAL SCIENCES

Recombination-dependent concatemeric viral DNA replication

(2011) Ambra Lo Piano et al.   VIRUS RESEARCH

Chromosomal Macrodomains and Associated Proteins: Implications for DNA Organization and Replication in Gram Negative Bacteria

(2011) Remus T. Dame et al.   PLoS Genetics

Eukaryotic Chromosome DNA Replication: Where, When, and How?

(2010) Hisao Masai et al.   Annual Review of Biochemistry

Does interference between replication and transcription contribute to genomic instability in cancer cells?

(2010) Sandie Tuduri et al.   CELL CYCLE

Is RecG a general guardian of the bacterial genome?

(2010) Christian J. Rudolph et al.   DNA REPAIR

Recruitment to stalled replication forks of the PriA DNA helicase and replisome-loading activities is essential for survival

(2010) Carolina B. Gabbai et al.   DNA REPAIR

The processing of double-stranded DNA breaks for recombinational repair by helicase–nuclease complexes

(2010) Joseph T.P. Yeeles et al.   DNA REPAIR

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

(2010) A. El Hage et al.   GENES & DEVELOPMENT

RecG Protein and Single-Strand DNA Exonucleases Avoid Cell Lethality Associated With PriA Helicase Activity in Escherichia coli

(2010) C. J. Rudolph et al.   GENETICS

Termination at sTop2

(2010) Robert C. Alver et al.   MOLECULAR CELL

Replication Termination at Eukaryotic Chromosomes Is Mediated by Top2 and Occurs at Genomic Loci Containing Pausing Elements

(2010) Daniele Fachinetti et al.   MOLECULAR CELL

Thymineless death is associated with loss of essential genetic information from the replication origin

(2010) Dipen P. Sangurdekar et al.   MOLECULAR MICROBIOLOGY

Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC

(2010) Tsutomu Katayama et al.   NATURE REVIEWS MICROBIOLOGY

Eukaryotic DNA replication origins: many choices for appropriate answers

(2010) Marcel Méchali   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Co-Orientation of Replication and Transcription Preserves Genome Integrity

(2010) Anjana Srivatsan et al.   PLoS Genetics

Defining replication origin efficiency using DNA fiber assays

(2009) Sandie Tuduri et al.   CHROMOSOME RESEARCH

The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

(2009) Hasna Boubakri et al.   EMBO JOURNAL

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes

(2009) Takashi Tadokoro et al.   FEBS Journal

Mechanisms of polar arrest of a replication fork

(2009) Daniel L. Kaplan et al.   MOLECULAR MICROBIOLOGY

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain

(2008) Romain Mercier et al.   CELL

The replication fork trap and termination of chromosome replication

(2008) Iain G. Duggin et al.   MOLECULAR MICROBIOLOGY

Patterns of chromosomal fragmentation due to uracil-DNA incorporation reveal a novel mechanism of replication-dependent double-stranded breaks

(2008) Elena A. Kouzminova et al.   MOLECULAR MICROBIOLOGY