H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation

(2019) Rupam Choudhury et al.   GENES & DEVELOPMENT

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

(2019) Evan D Tarbell et al.   NUCLEIC ACIDS RESEARCH

A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response

(2018) Takayuki Hoshii et al.   CELL

Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2

(2018) Martin R. Higgs et al.   MOLECULAR CELL

Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

(2018) Lorenzo Costantino et al.   MOLECULAR CELL

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

(2018) Apolinar Maya-Mendoza et al.   NATURE

A Metabolic Function for Phospholipid and Histone Methylation

(2017) Cunqi Ye et al.   MOLECULAR CELL

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

Transcription as a Threat to Genome Integrity

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

Is H3K4me3 instructive for transcription activation?

(2016) Françoise S. Howe et al.   BIOESSAYS

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

(2016) Stephan Hamperl et al.   CELL

Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription

(2015) Elizabeth A. Hoffman et al.   GENOME RESEARCH

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

An underlying mechanism for the increased mutagenesis of lagging-strand genes inBacillus subtilis

(2015) Samuel Million-Weaver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

(2015) Silvia Emma Rossi et al.   Cell Reports

Transcription-Associated Mutagenesis

(2014) Sue Jinks-Robertson et al.   Annual Review of Genetics

Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils

(2014) X. Fernandez et al.   EMBO JOURNAL

Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes

(2014) Gi-Moon Nam et al.   NUCLEIC ACIDS RESEARCH

H2B Mono-ubiquitylation Facilitates Fork Stalling and Recovery during Replication Stress by Coordinating Rad53 Activation and Chromatin Assembly

(2014) Chia-Yeh Lin et al.   PLoS Genetics

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

(2013) Jacqueline H. Barlow et al.   CELL

Accelerated gene evolution through replication–transcription conflicts

(2013) Sandip Paul et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

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

(2012) Ali Shilatifard   Annual Review of Biochemistry

DNA Replication Origin Function Is Promoted by H3K4 Di-methylation in Saccharomyces cerevisiae

(2012) L. F. Rizzardi et al.   GENETICS

G1/S and G2/M Cyclin-Dependent Kinase Activities Commit Cells to Death in the Absence of the S-Phase Checkpoint

(2012) N. Manfrini et al.   MOLECULAR AND CELLULAR BIOLOGY

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription as a source of genome instability

(2012) Nayun Kim et al.   NATURE REVIEWS GENETICS

Replication–transcription conflicts in bacteria

(2012) Houra Merrikh et al.   NATURE REVIEWS MICROBIOLOGY

Replication Fork Reversal after Replication–Transcription Collision

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

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

(2012) Thanasis Margaritis et al.   PLoS Genetics

The Replication Checkpoint Protects Fork Stability by Releasing Transcribed Genes from Nuclear Pores

(2011) Rodrigo Bermejo et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter

(2011) S.-S. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

(2011) Yaoting Gui et al.   NATURE GENETICS

Abasic Sites in the Transcribed Strand of Yeast DNA Are Removed by Transcription-Coupled Nucleotide Excision Repair

(2010) N. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome

(2010) Matthew D Sekedat et al.   Molecular Systems Biology

Phosphorylation of MLL by ATR is required for execution of mammalian S-phase checkpoint

(2010) Han Liu et al.   NATURE

Maintaining genome stability at the replication fork

(2010) Dana Branzei et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Replication and Active Demethylation Represent Partially Overlapping Mechanisms for Erasure of H3K4me3 in Budding Yeast

(2010) Marta Radman-Livaja et al.   PLoS Genetics

Methylated H3K4, a Transcription-Associated Histone Modification, Is Involved in the DNA Damage Response Pathway

(2010) David Faucher et al.   PLoS Genetics

Therapeutic targeting of MLL

(2009) M. Liedtke et al.   BLOOD

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

(2009) TaeSoo Kim et al.   CELL

Structural Insight Into Histone Recognition by the ING PHD Fingers

(2009) Karen Champagne et al.   CURRENT DRUG TARGETS

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

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

(2009) Hasna Boubakri et al.   EMBO JOURNAL

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

(2009) Anna Azvolinsky et al.   MOLECULAR CELL

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

An Oncogene-Induced DNA Damage Model for Cancer Development

(2008) T. D. Halazonetis et al.   SCIENCE