Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M

Transcription Restart Establishes Chromatin Accessibility after DNA Replication

(2019) Kathleen R. Stewart-Morgan et al.   MOLECULAR CELL

R-Loops Promote Antisense Transcription across the Mammalian Genome

(2019) Sue Mei Tan-Wong et al.   MOLECULAR CELL

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation

(2018) Johanna Fitz et al.   EMBO JOURNAL

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

(2018) Claire Marchal et al.   Nature Protocols

LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS

(2018) Li Li et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells

(2018) Nozomi Sugimoto et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Dynamic turnover of paused Pol II complexes at human promoters

(2018) Benjamin Erickson et al.   GENES & DEVELOPMENT

Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication

(2018) Nazaret Reverón-Gómez et al.   MOLECULAR CELL

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

(2018) Thomas Clouaire et al.   MOLECULAR CELL

High speed of fork progression induces DNA replication stress and genomic instability

(2018) Apolinar Maya-Mendoza et al.   NATURE

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

(2018) Morgane Macheret et al.   NATURE

An intrinsic S/G2 checkpoint enforced by ATR

(2018) Joshua C. Saldivar et al.   SCIENCE

Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing

(2018) Tobias Rausch et al.   BIOINFORMATICS

Transcription shapes DNA replication initiation and termination in human cells

(2018) Yu-Hung Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA repair factor RAD18 and DNA polymerase Polκ confer tolerance of oncogenic DNA replication stress

(2017) Yang Yang et al.   JOURNAL OF CELL BIOLOGY

RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells

(2017) Honglian Zhang et al.   MOLECULAR CELL

Mitotic transcription and waves of gene reactivation during mitotic exit

(2017) Katherine C. Palozola et al.   SCIENCE

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Transcription as a Threat to Genome Integrity

(2016) Hélène Gaillard et al.   Annual Review of Biochemistry

Conflict Resolution in the Genome: How Transcription and Replication Make It Work

(2016) Stephan Hamperl et al.   CELL

Mutation of cancer driverMLL2results in transcription stress and genome instability

(2016) Theodoros Kantidakis et al.   GENES & DEVELOPMENT

RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress

(2016) Rahul Bhowmick et al.   MOLECULAR CELL

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

(2016) Andreas Mayer et al.   Nature Protocols

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans

(2016) Ehsan Pourkarimi et al.   eLife

The chromatin environment shapes DNA replication origin organization and defines origin classes

(2015) Christelle Cayrou et al.   GENOME RESEARCH

The Human RNA Polymerase I Transcription Terminator Complex Acts as a Replication Fork Barrier That Coordinates the Progress of Replication with rRNA Transcription Activity

(2015) Yufuko Akamatsu et al.   MOLECULAR AND CELLULAR BIOLOGY

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

(2015) Kaiwei Liang et al.   MOLECULAR CELL

Replication stress activates DNA repair synthesis in mitosis

(2015) Sheroy Minocherhomji et al.   NATURE

DNA replication origin activation in space and time

(2015) Michalis Fragkos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

DNA synthesis by Pol η promotes fragile site stability by preventing under-replicated DNA in mitosis

(2013) Valérie Bergoglio et al.   JOURNAL OF CELL BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

(2012) Amaya Alzu et al.   CELL

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

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

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells

(2012) Jungmin Seo et al.   NUCLEIC ACIDS RESEARCH

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

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

(2011) Anne Helmrich et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

High-resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome

(2010) Jason S Iacovoni et al.   EMBO JOURNAL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription

(2009) Rodrigo Bermejo et al.   CELL

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY