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

UBR5 is co-amplified with MYC in breast tumors and encodes an ubiquitin ligase that limits MYC-dependent apoptosis

(2020) Xi Qiao et al.   CANCER RESEARCH

Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks

(2020) Sandeep Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Target gene-independent functions of MYC oncoproteins

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

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

Reactivation of Myc transcription in the mouse heart unlocks its proliferative capacity

(2020) Megan J. Bywater et al.   Nature Communications

Intrinsic cell-penetrating activity propels Omomyc from proof of concept to viable anti-MYC therapy

(2019) Marie-Eve Beaulieu et al.   Science Translational Medicine

Fanconi anemia protein FANCI functions in ribosome biogenesis

(2019) Samuel B. Sondalle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation

(2019) Alessandra Tesi et al.   EMBO REPORTS

Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations

(2019) Henrike Johanna Gothe et al.   MOLECULAR CELL

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

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

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

The DNA damage response to transcription stress

(2019) Hannes Lans et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc function

(2018) Jan B Heidelberger et al.   EMBO REPORTS

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

The Cellular Response to Transcription-Blocking DNA Damage

(2018) Lea H. Gregersen et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2018) Thomas Clouaire et al.   MOLECULAR CELL

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

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

(2018) Manpreet Kalkat et al.   MOLECULAR CELL

Transcription shapes DNA replication initiation and termination in human cells

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

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

Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation

(2017) Calla M Olson et al.   Nature Chemical Biology

PAF1 complex component Leo1 helps recruitDrosophilaMyc to promoters

(2017) Jennifer M. Gerlach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

E3 ubiquitin ligase Mule targets β-catenin under conditions of hyperactive Wnt signaling

(2017) Carmen Dominguez-Brauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello 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

The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6

(2016) S. Branden Van Oss et al.   MOLECULAR CELL

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

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

The TIP60 Complex Regulates Bivalent Chromatin Recognition by 53BP1 through Direct H4K20me Binding and H2AK15 Acetylation

(2016) Karine Jacquet et al.   MOLECULAR CELL

SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence

(2016) Luisa Tasselli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence

(2016) Luisa Tasselli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Different promoter affinities account for specificity in MYC-dependent gene regulation

(2016) Francesca Lorenzin et al.   eLife

A Novel CDK7 Inhibitor of the Pyrazolotriazine Class Exerts Broad-Spectrum Antiviral Activity at Nanomolar Concentrations

(2015) Corina Hutterer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

(2015) Janusz Puc et al.   CELL

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

Repression of SRF target genes is critical for Myc-dependent apoptosis of epithelial cells

(2015) K. E. Wiese et al.   EMBO JOURNAL

A mechanism for the suppression of homologous recombination in G1 cells

(2015) Alexandre Orthwein et al.   NATURE

The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc

(2015) Xiao-Xin Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional elongation requires DNA break-induced signalling

(2015) Heeyoun Bunch et al.   Nature Communications

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

(2014) Li Shen et al.   BMC GENOMICS

Tumor cell-specific inhibition of MYC function using small molecule inhibitors of the HUWE1 ubiquitin ligase

(2014) S. Peter et al.   EMBO Molecular Medicine

CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma

(2014) Chun-Hao Huang et al.   GENES & DEVELOPMENT

Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate

(2014) Gilad Fuchs et al.   GENOME RESEARCH

USP28 Is Recruited to Sites of DNA Damage by the Tandem BRCT Domains of 53BP1 but Plays a Minor Role in Double-Strand Break Metabolism

(2014) P. A. Knobel et al.   MOLECULAR AND CELLULAR BIOLOGY

ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression

(2014) Hong Wen et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

(2014) Arianna Sabò et al.   NATURE

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

(2014) Susanne Walz et al.   NATURE

Cancer Suppression by the Chromosome Custodians, BRCA1 and BRCA2

(2014) A. R. Venkitaraman   SCIENCE

Myc inhibition is effective against glioma and reveals a role for Myc in proficient mitosis

(2014) Daniela Annibali et al.   Nature Communications

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

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

MYC Activation Is a Hallmark of Cancer Initiation and Maintenance

(2014) M. Gabay et al.   Cold Spring Harbor Perspectives in Medicine

Inhibition of Myc family proteins eradicates KRas-driven lung cancer in mice

(2013) L. Soucek et al.   GENES & DEVELOPMENT

Histone chaperone FACT regulates homologous recombination by chromatin remodeling through interaction with RNF20

(2013) Douglas V. Oliveira et al.   JOURNAL OF CELL SCIENCE

Covalent and allosteric inhibitors of the ATPase VCP/p97 induce cancer cell death

(2013) Paola Magnaghi et al.   Nature Chemical Biology

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An Optimized microRNA Backbone for Effective Single-Copy RNAi

(2013) Christof Fellmann et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

TRIP12 and UBR5 Suppress Spreading of Chromatin Ubiquitylation at Damaged Chromosomes

(2012) Thorkell Gudjonsson et al.   CELL

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

A DNA hypermethylation module for the stem/progenitor cell signature of cancer

(2012) H. Easwaran et al.   GENOME RESEARCH

The chromatin remodeler p400 ATPase facilitates Rad51-mediated repair of DNA double-strand breaks

(2012) Céline Courilleau et al.   JOURNAL OF CELL BIOLOGY

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Deregulated MYC expression induces dependence upon AMPK-related kinase 5

(2012) Lidan Liu et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Regulation of Homologous Recombination by RNF20-Dependent H2B Ubiquitination

(2011) Kyosuke Nakamura et al.   MOLECULAR CELL

Requirement of ATM-Dependent Monoubiquitylation of Histone H2B for Timely Repair of DNA Double-Strand Breaks

(2011) Lilach Moyal et al.   MOLECULAR CELL

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs

(2010) Jonghwan Kim et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

(2010) Guoqiang Xu et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

RAD6-Mediated Transcription-Coupled H2B Ubiquitylation Directly Stimulates H3K4 Methylation in Human Cells

(2009) Jaehoon Kim et al.   CELL

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY