Histone crotonylation promotes mesoendodermal commitment of human embryonic stem cells

A novel case of ACOX2 deficiency leads to recognition of a third human peroxisomal acyl-CoA oxidase

(2018) Sacha Ferdinandusse et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile

(2018) Ryuichiro Nakato et al.   BIOINFORMATICS

Human Pluripotent Stem Cell-Derived Endoderm for Modeling Development and Clinical Applications

(2018) Loukia Yiangou et al.   Cell Stem Cell

HIV latency is reversed by ACSS2-driven histone crotonylation

(2018) Guochun Jiang et al.   JOURNAL OF CLINICAL INVESTIGATION

p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis

(2018) He Huang et al.   MOLECULAR CELL

Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells

(2018)   Nature Communications

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases

(2018) Rachel Fellows et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Germline mutations affecting the histone H4 core cause a developmental syndrome by altering DNA damage response and cell cycle control

(2017) Federico Tessadori et al.   NATURE GENETICS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Characterization of histone acylations links chromatin modifications with metabolism

(2017) Johayra Simithy et al.   Nature Communications

LC-quadrupole/Orbitrap high-resolution mass spectrometry enables stable isotope-resolved simultaneous quantification and 13C-isotopic labeling of acyl-coenzyme A thioesters

(2016) Alexander J. Frey et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

YEATS2 is a selective histone crotonylation reader

(2016) Dan Zhao et al.   CELL RESEARCH

Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State

(2016) Wen Gu et al.   Cell Stem Cell

Histone lysine crotonylation during acute kidney injury in mice

(2016) Olga Ruiz-Andres et al.   Disease Models & Mechanisms

Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain

(2016) Yuanyuan Li et al.   MOLECULAR CELL

Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2

(2016) Xiaozhe Xiong et al.   Nature Chemical Biology

The Taf14 YEATS domain is a reader of histone crotonylation

(2016) Forest H Andrews et al.   Nature Chemical Biology

Metabolic regulation of gene expression through histone acylations

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

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Lateral Thinking: How Histone Modifications Regulate Gene Expression

(2016) Moyra Lawrence et al.   TRENDS IN GENETICS

Glycolysis-Mediated Changes in Acetyl-CoA and Histone Acetylation Control the Early Differentiation of Embryonic Stem Cells

(2015) Arieh Moussaieff et al.   Cell Metabolism

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

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

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

(2015) Mathieu Dalvai et al.   Cell Reports

Methionine Metabolism Regulates Maintenance and Differentiation of Human Pluripotent Stem Cells

(2014) Nobuaki Shiraki et al.   Cell Metabolism

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9

(2014) A. Stolfi et al.   DEVELOPMENT

Unfolded Protein Response Is Required for the Definitive Endodermal Specification of Mouse Embryonic Stem Cells via Smad2 and β-Catenin Signaling

(2014) Huiming Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells

(2014) Bryce W. Carey et al.   NATURE

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Metabolic requirements for the maintenance of self-renewing stem cells

(2014) Keisuke Ito et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach

(2014) Xiucong Bao et al.   eLife

Activation of the amino acid response modulates lineage specification during differentiation of murine embryonic stem cells

(2013) Jixiu Shan et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Profiling of Substrates for Zinc-dependent Lysine Deacylase Enzymes: HDAC3 Exhibits Decrotonylase Activity In Vitro

(2012) Andreas S. Madsen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Metabolic Regulation in Pluripotent Stem Cells during Reprogramming and Self-Renewal

(2012) Jin Zhang et al.   Cell Stem Cell

Metabolic Plasticity in Stem Cell Homeostasis and Differentiation

(2012) Clifford D.L. Folmes et al.   Cell Stem Cell

RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in post-meiotic spermatids

(2012) H.-S. Sin et al.   GENES & DEVELOPMENT

Influence of Threonine Metabolism on S-Adenosylmethionine and Histone Methylation

(2012) N. Shyh-Chang et al.   SCIENCE

Histone crotonylation specifically marks the haploid male germ cell gene expression program

(2011) Emilie Montellier et al.   BIOESSAYS

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER CELL

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

(2011) Minjia Tan et al.   CELL

Somatic Oxidative Bioenergetics Transitions into Pluripotency-Dependent Glycolysis to Facilitate Nuclear Reprogramming

(2011) Clifford D.L. Folmes et al.   Cell Metabolism

The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

(2011) Athanasia D Panopoulos et al.   CELL RESEARCH

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

SILEC: a protocol for generating and using isotopically labeled coenzyme A mass spectrometry standards

(2011) Sankha S Basu et al.   Nature Protocols

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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