Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

APOBEC3B mutagenesis in cancer

(2013) Kawai J Kuong et al.   NATURE GENETICS

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Binding of RNA by APOBEC3G controls deamination-independent restriction of retroviruses

(2013) Kasandra Bélanger et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Mutation Avalanches Induced in Diploid Yeast Cells by a Base Analog or an APOBEC Deaminase

(2013) Artem G. Lada et al.   PLoS Genetics

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries

(2012) Alessandro Vannini   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

A role for the RNA pol II–associated PAF complex in AID-induced immune diversification

(2012) Katharina L. Willmann et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A Combined Nuclear and Nucleolar Localization Motif in Activation-Induced Cytidine Deaminase (AID) Controls Immunoglobulin Class Switching

(2012) Yi Hu et al.   JOURNAL OF MOLECULAR BIOLOGY

Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries

(2012) Alessandro Vannini et al.   MOLECULAR CELL

Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions

(2012) Steven A. Roberts 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

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening

(2012) Sebastian Grünberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

AID targeting is dependent on RNA polymerase II pausing

(2012) Amy L. Kenter   SEMINARS IN IMMUNOLOGY

The role of FACT in making and breaking nucleosomes

(2011) Tim Formosa   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Translocation-Capture Sequencing Reveals the Extent and Nature of Chromosomal Rearrangements in B Lymphocytes

(2011) Isaac A. Klein et al.   CELL

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

(2011) Roberto Chiarle et al.   CELL

The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates

(2011) Uttiya Basu et al.   CELL

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

(2011) Bryan J. Venters et al.   MOLECULAR CELL

Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity

(2011) T. Wongsurawat et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation

(2011) I.-m. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5

(2010) Rushad Pavri et al.   CELL

DNA ligase 4 stabilizes the ribosomal DNA array upon fork collapse at the replication fork barrier

(2010) Olivier Fritsch et al.   DNA REPAIR

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes

(2010) Arito Yamane et al.   NATURE IMMUNOLOGY

Gene-specific RNA polymerase II phosphorylation and the CTD code

(2010) Hyunmin Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity

(2009) Meng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA-Dependent Oligomerization of APOBEC3G Is Required for Restriction of HIV-1

(2009) Hendrik Huthoff et al.   PLoS Pathogens

Restricting activation-induced cytidine deaminase tumorigenic activity in B lymphocytes

(2008) Rafael Casellas et al.   IMMUNOLOGY

Two levels of protection for the B cell genome during somatic hypermutation

(2008) Man Liu et al.   NATURE

Variable contexts and levels of hypermutation in HIV-1 proviral genomes recovered from primary peripheral blood mononuclear cells

(2008) Gustavo H. Kijak et al.   VIROLOGY