BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications

(2021) Vignesh Kasinath et al.   SCIENCE

Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy

(2021) Miles K. Huseyin et al.   Nature Communications

Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions

(2020) Idan Cohen et al.   BIOESSAYS

RYBP/YAF2-PRC1 complexes and histone H1-dependent chromatin compaction mediate propagation of H2AK119ub1 during cell division

(2020) Jicheng Zhao et al.   NATURE CELL BIOLOGY

PR-DUB maintains expression of critical genes through FOXK1/2 and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination

(2020) Petros Kolovos et al.   GENOME RESEARCH

Enhancer RNAs are an important regulatory layer of the epigenome

(2020) Vittorio Sartorelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

(2020) Aileen Patricia Szczepanski et al.   Genome Medicine

Regulation of Histone Ubiquitination in Response to DNA Double Strand Breaks

(2020) Lanni Aquila et al.   Cells

BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation

(2019) Antoine Campagne et al.   Nature Communications

Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer

(2019) Adrian P. Bracken et al.   GENES & DEVELOPMENT

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities

(2019) Andrea Scelfo et al.   MOLECULAR CELL

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression

(2019) Nadezda A. Fursova et al.   MOLECULAR CELL

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

(2019) Anne H Turberfield et al.   NUCLEIC ACIDS RESEARCH

Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation

(2019) Tatyana B. Nesterova et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

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

The role of Xist ‐mediated Polycomb recruitment in the initiation of X‐chromosome inactivation

(2019) Aurélie Bousard et al.   EMBO REPORTS

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

BAP1 regulates epigenetic switch from pluripotency to differentiation in developmental lineages giving rise to BAP1-mutant cancers

(2019) Jeffim N. Kuznetsov et al.   Science Advances

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression

(2019) Simone Tamburri et al.   MOLECULAR CELL

PRC1 Catalytic Activity Is Central to Polycomb System Function

(2019) Neil P. Blackledge et al.   MOLECULAR CELL

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding

(2018) Matteo Perino et al.   NATURE GENETICS

Resetting the epigenetic balance of Polycomb and COMPASS function at enhancers for cancer therapy

(2018) Lu Wang et al.   NATURE MEDICINE

Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes

(2018) Hamish W. King et al.   GENOME RESEARCH

The Implication of Early Chromatin Changes in X Chromosome Inactivation

(2018) Jan Jakub Żylicz et al.   CELL

Ubiquitination-Independent Repression of PRC1 Targets during Neuronal Fate Restriction in the Developing Mouse Neocortex

(2018) Masafumi Tsuboi et al.   DEVELOPMENTAL CELL

Chromatin and nucleosome dynamics in DNA damage and repair

(2017) Michael H. Hauer et al.   GENES & DEVELOPMENT

Polycomb-like proteins link the PRC2 complex to CpG islands

(2017) Haojie Li et al.   NATURE

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

The interplay of epigenetic marks during stem cell differentiation and development

(2017) Yaser Atlasi et al.   NATURE REVIEWS GENETICS

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Emerging roles of linker histones in regulating chromatin structure and function

(2017) Dmitry V. Fyodorov et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing

(2017) Zhuo Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Additional sex combs interacts with enhancer of zeste and trithorax and modulates levels of trimethylation on histone H3K4 and H3K27 during transcription of hsp70

(2017) Taosui Li et al.   Epigenetics & Chromatin

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1

(2016) Hitoshi Aihara et al.   MOLECULAR CELL

Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals

(2016) Hui Zheng et al.   MOLECULAR CELL

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation

(2016) Susan L Kloet et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements

(2016) Tatyana G. Kahn et al.   NUCLEIC ACIDS RESEARCH

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Histone Modifications and Cancer

(2016) James E. Audia et al.   Cold Spring Harbor Perspectives in Biology

Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2

(2016) Sarah Cooper et al.   Nature Communications

BAP1/ASXL1 recruitment and activation for H2A deubiquitination

(2016) Danny D. Sahtoe et al.   Nature Communications

The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation

(2016) Susan L Kloet et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A High-Density Map for Navigating the Human Polycomb Complexome

(2016) Simon Hauri et al.   Cell Reports

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes

(2016) Nathan R Rose et al.   eLife

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination

(2015) Weihua Qin et al.   CELL RESEARCH

Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals

(2015) Xudong Wu et al.   CELL RESEARCH

Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms

(2015) Lluis Morey et al.   Cell Stem Cell

The quest for mammalian Polycomb response elements: are we there yet?

(2015) Moritz Bauer et al.   CHROMOSOMA

The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development

(2015) Robert S. Illingworth et al.   GENES & DEVELOPMENT

Genome-wide activities of Polycomb complexes control pervasive transcription

(2015) Hun-Goo Lee et al.   GENOME RESEARCH

The BAP1/ASXL2 Histone H2A Deubiquitinase Complex Regulates Cell Proliferation and Is Disrupted in Cancer

(2015) Salima Daou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

(2015) Neil P. Blackledge et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive Catalog of Currently Documented Histone Modifications

(2015) Yingming Zhao et al.   Cold Spring Harbor Perspectives in Biology

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation

(2014) Neil P. Blackledge et al.   CELL

H2A-DUBbing the mammalian epigenome: Expanding frontiers for histone H2A deubiquitinating enzymes in cell biology and physiology

(2014) Jad I. Belle et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards

(2014) Jacek R. Wiśniewski et al.   MOLECULAR & CELLULAR PROTEOMICS

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Comparative analysis of metazoan chromatin organization

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

Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression

(2014) Reinhard Kalb et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Targeting Polycomb to Pericentric Heterochromatin in Embryonic Stem Cells Reveals a Role for H2AK119u1 in PRC2 Recruitment

(2014) Sarah Cooper et al.   Cell Reports

Readout of Epigenetic Modifications

(2013) Dinshaw J. Patel et al.   Annual Review of Biochemistry

Functional and cancer genomics of ASXL family members

(2013) M Katoh   BRITISH JOURNAL OF CANCER

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Fbxl10/Kdm2b Recruits Polycomb Repressive Complex 1 to CpG Islands and Regulates H2A Ubiquitylation

(2013) Xudong Wu et al.   MOLECULAR CELL

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes

(2013) Jin He et al.   NATURE CELL BIOLOGY

Chromatin Sampling—An Emerging Perspective on Targeting Polycomb Repressor Proteins

(2013) Robert J. Klose et al.   PLoS Genetics

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

MicroRNA Regulation of Cbx7 Mediates a Switch of Polycomb Orthologs during ESC Differentiation

(2012) Ana O'Loghlen et al.   Cell Stem Cell

Nonoverlapping Functions of the Polycomb Group Cbx Family of Proteins in Embryonic Stem Cells

(2012) Lluis Morey et al.   Cell Stem Cell

Histone H2A monoubiquitination and Polycomb repression

(2012) Johanna C. Scheuermann et al.   FLY

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Polycomb Repressive Complex 1 (PRC1) Disassembles RNA Polymerase II Preinitiation Complexes

(2012) Lynn Lehmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

(2012) Stéphane Larochelle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tumours associated with BAP1 mutations

(2012) Rajmohan Murali et al.   PATHOLOGY

Loss of the Tumor Suppressor BAP1 Causes Myeloid Transformation

(2012) A. Dey et al.   SCIENCE

Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity

(2012) Mitsuhiro Endoh et al.   PLoS Genetics

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

(2012) Anca M Farcas et al.   eLife

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Germline mutations in BAP1 predispose to melanocytic tumors

(2011) Thomas Wiesner et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The DUBle Life of Polycomb Complexes

(2010) Bernd Schuettengruber et al.   DEVELOPMENTAL CELL

The Ubiquitin Carboxyl Hydrolase BAP1 Forms a Ternary Complex with YY1 and HCF-1 and Is a Critical Regulator of Gene Expression

(2010) H. Yu et al.   MOLECULAR AND CELLULAR BIOLOGY

The Chromatin Signaling Pathway: Diverse Mechanisms of Recruitment of Histone-Modifying Enzymes and Varied Biological Outcomes

(2010) Edwin Smith et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB

(2010) Johanna C. Scheuermann et al.   NATURE

Transcriptional activation of polycomb-repressed genes by ZRF1

(2010) Holger Richly et al.   NATURE

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae

(2009) Kitty F Verzijlbergen et al.   BMC MOLECULAR BIOLOGY

Additional sex combs-like 1 belongs to the enhancer of trithorax and polycomb group and genetically interacts with Cbx2 in mice

(2009) C.L. Fisher et al.   DEVELOPMENTAL BIOLOGY

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Functional Conservation of Asxl2, a Murine Homolog for the Drosophila Enhancer of Trithorax and Polycomb Group Gene Asx

(2009) Heather A. Baskind et al.   PLoS One

BRCA1-Associated Protein-1 Is a Tumor Suppressor that Requires Deubiquitinating Activity and Nuclear Localization

(2008) K. H. Ventii et al.   CANCER RESEARCH

Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation

(2008) T. Nakagawa et al.   GENES & DEVELOPMENT

Histone H2A Monoubiquitination Represses Transcription by Inhibiting RNA Polymerase II Transcriptional Elongation

(2008) Wenlai Zhou et al.   MOLECULAR CELL

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY