Histone propionylation is a mark of active chromatin

Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation

(2016) Zhongyu Xie et al.   MOLECULAR CELL

Dynamic Competing Histone H4 K5K8 Acetylation and Butyrylation Are Hallmarks of Highly Active Gene Promoters

(2016) Afsaneh Goudarzi et al.   MOLECULAR CELL

Structure of p300 in complex with acyl-CoA variants

(2016) Zuzanna Kaczmarska et al.   Nature Chemical Biology

Metabolic regulation of gene expression through histone acylations

(2016) Benjamin R. Sabari et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Structural basis for acyl-group discrimination by human Gcn5L2

(2016) Alison E. Ringel et al.   Acta Crystallographica Section D-Structural Biology

Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation

(2015) Benjamin R. Sabari et al.   MOLECULAR CELL

Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation

(2015) Serena Sanulli et al.   MOLECULAR CELL

Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

(2015) Renaud Vincentelli et al.   NATURE METHODS

Standardizing chromatin research: a simple and universal method for ChIP-seq

(2015) Laura Arrigoni et al.   NUCLEIC ACIDS RESEARCH

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance

(2015) O. Fedorov et al.   Science Advances

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

(2014) S. Anders et al.   BIOINFORMATICS

SnapShot: Histone Modifications

(2014) He Huang et al.   CELL

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

(2014) Jacques Bonnet et al.   GENES & DEVELOPMENT

Aberrant protein acylation is a common observation in inborn errors of acyl-CoA metabolism

(2014) Olga Pougovkina et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

(2014) Lunzhi Dai et al.   Nature Chemical Biology

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription

(2014) Vincenzo Di Cerbo et al.   eLife

Regulation of Transcription through Acetylation of H3K122 on the Lateral Surface of the Histone Octamer

(2013) Philipp Tropberger et al.   CELL

Influence of Metabolism on Epigenetics and Disease

(2013) William G. Kaelin et al.   CELL

Generation of a Hypomorphic Model of Propionic Acidemia Amenable to Gene Therapy Testing

(2013) Adam J Guenzel et al.   MOLECULAR THERAPY

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Protein Lysine Acylation and Cysteine Succination by Intermediates of Energy Metabolism

(2012) Hening Lin et al.   ACS Chemical Biology

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

(2012) Krishanpal Karmodiya et al.   BMC GENOMICS

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

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

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Lysine Succinylation and Lysine Malonylation in Histones

(2012) Zhongyu Xie et al.   MOLECULAR & CELLULAR PROTEOMICS

Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects

(2012) Andrew A. Palladino et al.   MOLECULAR GENETICS AND METABOLISM

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

(2012) Yin Shen et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

linking metabolism to epigenetics through O-GlcNAcylation

(2012) John A. Hanover et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Perceiving the epigenetic landscape through histone readers

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

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

SnapShot: Chromatin Remodeling:SWI/SNF

(2011) Margaret M. Kasten et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Interaction of Propionylated and Butyrylated Histone H3 Lysine Marks with Brd4 Bromodomains

(2010) Friederike Vollmuth et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

KAT(ching) Metabolism by the Tail: Insight into the Links between Lysine Acetyltransferases and Metabolism

(2010) Brittany N. Albaugh  et al.   CHEMBIOCHEM

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

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

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Human Histone Acetyltransferase P/CAF is a Promiscuous Histone Propionyltransferase

(2008) Hans Leemhuis et al.   CHEMBIOCHEM

Ezh1 and Ezh2 Maintain Repressive Chromatin through Different Mechanisms

(2008) Raphael Margueron et al.   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY