Dynamic profiling and functional interpretation of histone lysine crotonylation and lactylation during neural development

Class I histone deacetylases (HDAC1–3) are histone lysine delactylases

(2022) Carlos Moreno-Yruela et al.   Science Advances

Histone crotonylation promotes mesoendodermal commitment of human embryonic stem cells

(2021) Yi Fang et al.   Cell Stem Cell

Transcription shapes genome-wide histone acetylation patterns

(2021) Benjamin J. E. Martin et al.   Nature Communications

Short-Chain Enoyl-CoA Hydratase Mediates Histone Crotonylation and Contributes to Cardiac Homeostasis

(2021) Xiaoqiang Tang et al.   CIRCULATION

Histone crotonylation-centric gene regulation

(2021) Kun Li et al.   Epigenetics & Chromatin

The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway

(2021) He Huang et al.   Science Advances

Histone crotonylation regulates neural stem cell fate decisions by activating bivalent promoters

(2021) Shang‐Kun Dai et al.   EMBO REPORTS

Chromatin as a key consumer in the metabolite economy

(2020) Katharine L. Diehl et al.   Nature Chemical Biology

Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes

(2020) Marion Crespo et al.   NUCLEIC ACIDS RESEARCH

Release of promoter–proximal paused Pol II in response to histone deacetylase inhibition

(2020) Roshan Vaid et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Michal Lipinski et al.   Nature Communications

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

HDAC1 and HDAC2 Regulate Intermediate Progenitor Positioning to Safeguard Neocortical Development

(2019) Tianxiang Tang et al.   NEURON

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription

(2019) Leonie Kollenstart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic regulation of gene expression by histone lactylation

(2019) Di Zhang et al.   NATURE

Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression

(2019) Graeme J. Gowans et al.   MOLECULAR CELL

HIV latency is reversed by ACSS2-driven histone crotonylation

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

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

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

Regulation of chromatin and gene expression by metabolic enzymes and metabolites

(2018) Xinjian Li et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2018) Rachel Fellows et al.   Nature Communications

Lysine benzoylation is a histone mark regulated by SIRT2

(2018) He Huang et al.   Nature Communications

Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo

(2018) R. D. W. Kelly et al.   Scientific Reports

Chromodomain Y-like Protein–Mediated Histone Crotonylation Regulates Stress-Induced Depressive Behaviors

(2018) Yongqing Liu et al.   BIOLOGICAL PSYCHIATRY

Mitochondria as central regulators of neural stem cell fate and cognitive function

(2018) Mireille Khacho et al.   NATURE REVIEWS NEUROSCIENCE

Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis

(2017) Shumeng Liu et al.   MOLECULAR CELL

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Birth and Death of Histone mRNAs

(2017) William F. Marzluff et al.   TRENDS IN GENETICS

Dynamics of RNA Polymerase II Pausing and Bivalent Histone H3 Methylation during Neuronal Differentiation in Brain Development

(2017) Jiancheng Liu et al.   Cell Reports

MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300

(2017) Xiaoguang Liu et al.   Cell Discovery

YEATS2 is a selective histone crotonylation reader

(2016) Dan Zhao et al.   CELL RESEARCH

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

Epigenetic mechanisms in neurogenesis

(2016) Bing Yao et al.   NATURE REVIEWS NEUROSCIENCE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Guangchuang Yu et al.   BIOINFORMATICS

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation

(2014) Yuanyuan Li et al.   CELL

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The super elongation complex (SEC) family in transcriptional control

(2012) Zhuojuan Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

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

(2011) Minjia Tan et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

CBP Histone Acetyltransferase Activity Regulates Embryonic Neural Differentiation in the Normal and Rubinstein-Taybi Syndrome Brain

(2010) Jing Wang et al.   DEVELOPMENTAL CELL

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