Readout of histone methylation by Trim24 locally restricts chromatin opening by p53

monaLisa: an R/Bioconductor package for identifying regulatory motifs

(2022) Dania Machlab et al.   BIOINFORMATICS

Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance

(2022) Jan Padeken et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mammalian SWI/SNF continuously restores local accessibility to chromatin

(2021) Mario Iurlaro et al.   NATURE GENETICS

BANP opens chromatin and activates CpG-island-regulated genes

(2021) Ralph S. Grand et al.   NATURE

The molecular principles of gene regulation by Polycomb repressive complexes

(2021) Neil P. Blackledge et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes

(2021) Nazar Mashtalir et al.   SCIENCE

A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer

(2021) Marc A.J. Morgan et al.   GENES & DEVELOPMENT

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(2021) Luis F. Soto et al.   MOLECULAR CELL

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

(2020) Kanishk Jain et al.   Epigenetics & Chromatin

TRIM24 facilitates antiviral immunity through mediating K63-linked TRAF3 ubiquitination

(2020) Qingchen Zhu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

(2020) Alicia K. Michael et al.   SCIENCE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

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(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns

(2019) Divyanshi Srivastava et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands

(2018) Lara N. Gechijian et al.   Nature Chemical Biology

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

(2017) Geoffrey P. Dann et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

p53 regulates enhancer accessibility and activity in response to DNA damage

(2017) Scott T. Younger et al.   NUCLEIC ACIDS RESEARCH

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

The Transcriptional Landscape of p53 Signalling Pathway

(2017) Chizu Tanikawa et al.   EBioMedicine

TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer

(2016) Anna C. Groner et al.   CANCER CELL

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

p53 genes function to restrain mobile elements

(2015) Annika Wylie et al.   GENES & DEVELOPMENT

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53

(2015) H Yan et al.   Cell Death & Disease

Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo

(2015) Claudia Tonelli et al.   Oncotarget

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome

(2015) Luke Isbel et al.   PLoS Genetics

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Structural insights into the TRIM family of ubiquitin E3 ligases

(2014) Yang Li et al.   CELL RESEARCH

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

(2014) Morgan A. Sammons et al.   GENOME RESEARCH

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Trim24-repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA

(2013) Benjamin Herquel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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(2013) Michael Lawrence et al.   PLoS Computational Biology

The Ubiquitin Code

(2012) David Komander et al.   Annual Review of Biochemistry

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

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Ectopic Expression of Neurogenin 2 Alone is Sufficient to Induce Differentiation of Embryonic Stem Cells into Mature Neurons

(2012) Eva C. Thoma et al.   PLoS One

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

The p53 response element and transcriptional repression

(2011) Bei Wang et al.   CELL CYCLE

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Histone fold modifications control nucleosome unwrapping and disassembly

(2011) M. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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(2011) Steven Henikoff et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

TRIM24 links a non-canonical histone signature to breast cancer

(2010) Wen-Wei Tsai et al.   NATURE

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

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

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

Structural Insight Into Histone Recognition by the ING PHD Fingers

(2009) Karen Champagne et al.   CURRENT DRUG TARGETS

A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics

(2009) A. M. Quinn et al.   NUCLEIC ACIDS RESEARCH

A genomewide study identifies the Wnt signaling pathway as a major target of p53 in murine embryonic stem cells

(2009) K.-H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trim24 targets endogenous p53 for degradation

(2009) Kendra Allton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies

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The COXIB Experience: A Look in the Rearview Mirror

(2008) Lawrence J. Marnett   Annual Review of Pharmacology and Toxicology

Histone H3K4me3 Binding Is Required for the DNA Repair and Apoptotic Activities of ING1 Tumor Suppressor

(2008) P.V. Peña et al.   JOURNAL OF MOLECULAR BIOLOGY

Multivalent Binding of p53 to the STAGA Complex Mediates Coactivator Recruitment after UV Damage

(2008) A. M. Gamper et al.   MOLECULAR AND CELLULAR BIOLOGY

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL