Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release

Enhancers predominantly regulate gene expression during differentiation via transcription initiation

(2021) Martin S.C. Larke et al.   MOLECULAR CELL

Using TTchem-seq for profiling nascent transcription and measuring transcript elongation

(2020) Lea H. Gregersen et al.   Nature Protocols

KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain

(2020) Michal Lipinski et al.   Nature Communications

Histone deacetylases 1 and 2 silence cryptic transcription to promote mitochondrial function during cardiogenesis

(2020) Zachary J. Milstone et al.   Science Advances

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming

(2019) Ayyub Ebrahimi et al.   Nature Chemical Biology

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

TAF1 plays a critical role in AML1-ETO driven leukemogenesis

(2019) Ye Xu et al.   Nature Communications

EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations

(2018) Zuguang Gu et al.   BMC GENOMICS

Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

(2018) Brian T. Weinert et al.   CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2018) Matthias Muhar et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

TissueEnrich: Tissue-specific gene enrichment analysis

(2018) Ashish Jain et al.   BIOINFORMATICS

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Structure of human TFIID and mechanism of TBP loading onto promoter DNA

(2018) Avinash B. Patel et al.   SCIENCE

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

(2017) Loren M. Lasko et al.   NATURE

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

BET Bromodomain Inhibition Releases the Mediator Complex from Select cis -Regulatory Elements

(2016) Anand S. Bhagwat et al.   Cell Reports

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

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

(2015) Nancy Yiu-Lin Yu et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

(2015) Cameron Sokolik et al.   Cell Systems

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Li Shen et al.   BMC GENOMICS

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

(2014) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Transcriptional/epigenetic regulator CBP/p300 in tumorigenesis: structural and functional versatility in target recognition

(2013) Feng Wang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

(2013) Eliezer Calo et al.   MOLECULAR CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition

(2013) Jose P. Lopez-Atalaya et al.   NUCLEIC ACIDS RESEARCH

Multivalent Engagement of TFIID to Nucleosomes

(2013) Rick van Nuland et al.   PLoS One

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

(2013) Brian T. Weinert et al.   Cell Reports

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation

(2013) Ji-Eun Lee et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CBP and p300 are essential for renin cell identity and morphological integrity of the kidney

(2009) R. Ariel Gomez et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

Therapeutic application of histone deacetylase inhibitors for central nervous system disorders

(2008) Aleksey G. Kazantsev et al.   NATURE REVIEWS DRUG DISCOVERY

Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300

(2008) Lei Zeng et al.   STRUCTURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY