MYCN recruits the nuclear exosome complex to RNA polymerase II to prevent transcription-replication conflicts

Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters

(2021) Theresa Endres et al.   MOLECULAR CELL

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

(2021) Aleix Bayona-Feliu et al.   NATURE GENETICS

Target gene-independent functions of MYC oncoproteins

(2020) Apoorva Baluapuri et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Splice or Die: When MYC Is Driving, Transcription Needs NUAK1 to Avoid Fatal Pileups

(2020) Robert P. Fisher   MOLECULAR CELL

Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations

(2020) Samuel W. Brady et al.   Nature Communications

Causes and consequences of RNA polymerase II stalling during transcript elongation

(2020) Melvin Noe Gonzalez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription factor regulation of RNA polymerase’s torque generation capacity

(2019) Jie Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control

(2019) Lee Davidson et al.   Cell Reports

Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase

(2019) Steffi Herold et al.   NATURE

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

(2019) Apoorva Baluapuri et al.   MOLECULAR CELL

High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing

(2019) Lionel A. Sanz et al.   Nature Protocols

EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks

(2019) Judit Domingo-Prim et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

(2019) Diana Zatreanu et al.   MOLECULAR CELL

The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay

(2019) Toomas Silla et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

(2018) Anthony C. Chiu et al.   MOLECULAR CELL

Decapping protein EDC4 regulates DNA repair and phenocopies BRCA1

(2018) Gonzalo Hernández et al.   Nature Communications

The Expanding World of N-MYC–Driven Tumors

(2018) David S. Rickman et al.   Cancer Discovery

EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma

(2018) Aparna Gorthi et al.   NATURE

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

(2018) Morgane Macheret et al.   NATURE

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan et al.   MOLECULAR CELL

MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis

(2018) Manpreet Kalkat et al.   MOLECULAR CELL

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

(2017) John C. Zinder et al.   GENES & DEVELOPMENT

Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

(2017) Stefano de Pretis et al.   GENOME RESEARCH

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Prediction of potent shRNAs with a sequential classification algorithm

(2017) Raphael Pelossof et al.   NATURE BIOTECHNOLOGY

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis

(2017) Xiaowen Zhang et al.   Nature Communications

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

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

Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle

(2017) Gabriele Büchel et al.   Cell Reports

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

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

(2016) Stephan Hamperl et al.   CELL

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

(2016) Jérôme Poli et al.   GENES & DEVELOPMENT

Ubiquitin-Dependent Turnover of MYC Antagonizes MYC/PAF1C Complex Accumulation to Drive Transcriptional Elongation

(2016) Laura A. Jaenicke et al.   MOLECULAR CELL

Transcription–replication conflicts: how they occur and how they are resolved

(2016) Tatiana García-Muse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The regulation and functions of the nuclear RNA exosome complex

(2016) Cornelia Kilchert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double-Stranded Structured RNAs

(2015) Sara Macias et al.   MOLECULAR CELL

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles

(2014) Susanne Walz et al.   NATURE

The RNA exosome promotes transcription termination of backtracked RNA polymerase II

(2014) Jean-François Lemay et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cancer Suppression by the Chromosome Custodians, BRCA1 and BRCA2

(2014) A. R. Venkitaraman   SCIENCE

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage

(2013) P. Richard et al.   GENES & DEVELOPMENT

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

An Optimized microRNA Backbone for Effective Single-Copy RNAi

(2013) Christof Fellmann et al.   Cell Reports

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

Activities of human RRP6 and structure of the human RRP6 catalytic domain

(2011) K. Januszyk et al.   RNA

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Improved ATM kinase inhibitor KU-60019 radiosensitizes glioma cells, compromises insulin, AKT and ERK prosurvival signaling, and inhibits migration and invasion

(2009) S. E. Golding et al.   MOLECULAR CANCER THERAPEUTICS