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

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

NEAT1 regulates neuroglial cell mediating Aβ clearance via the epigenetic regulation of endocytosis-related genes expression

(2019) Ziqiang Wang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Molecular basis for hierarchical histone de-β-hydroxybutyrylation by SIRT3

(2019) Xingrun Zhang et al.   Cell Discovery

Distinct H3K9me3 and DNA methylation modifications during mouse spermatogenesis

(2019) Yingdong Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic regulation of gene expression by histone lactylation

(2019) Di Zhang et al.   NATURE

The transcription factor SOX30 is a key regulator of mouse spermiogenesis

(2018) Daoqin Zhang et al.   DEVELOPMENT

Sox30 initiates transcription of haploid genes during late meiosis and spermiogenesis in mouse testes

(2018) Shun Bai et al.   DEVELOPMENT

HIV latency is reversed by ACSS2-driven histone crotonylation

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

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

(2018) Benjamin R. Sabari et al.   MOLECULAR CELL

p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis

(2018) He Huang et al.   MOLECULAR CELL

Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation

(2018) Yi Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal Control of Acetyl-CoA Metabolism in Chromatin Regulation

(2018) Sharanya Sivanand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions

(2018) Kosuke Yamaguchi et al.   Cell Reports

BRDT is an essential epigenetic regulator for proper chromatin organization, silencing of sex chromosomes and crossover formation in male meiosis

(2018) Marcia Manterola et al.   PLoS Genetics

RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes

(2018) Shannel R. Adams et al.   PLoS Genetics

An Efficient Approach for Selective Enrichment of Histone Modification Readers Using Self-Assembled Multivalent Photoaffinity Peptide Probes

(2018) Guijin Zhai et al.   ANALYTICAL CHEMISTRY

Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis

(2018) Yao Chen et al.   CELL RESEARCH

Lysine benzoylation is a histone mark regulated by SIRT2

(2018) He Huang et al.   Nature Communications

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

(2018) Ryan Raisner et al.   Cell Reports

Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells

(2018) Hitoshi Shiota et al.   Cell Reports

Beyond histone acetylation—writing and erasing histone acylations

(2018) Shuai Zhao et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells

(2017) Sophie Barral et al.   MOLECULAR CELL

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

(2017) Shumeng Liu et al.   MOLECULAR CELL

KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase

(2017) Yugang Wang et al.   NATURE

Histone propionylation is a mark of active chromatin

(2017) Adam F Kebede et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers

(2017) Monica Soldi et al.   NUCLEIC ACIDS RESEARCH

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

(2017) Sara El Kennani et al.   Epigenetics & Chromatin

YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer

(2017) Wenyi Mi et al.   Nature Communications

Characterization of histone acylations links chromatin modifications with metabolism

(2017) Johayra Simithy et al.   Nature Communications

Histone propionylation is a mark of active chromatin

(2017) Adam F Kebede et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SOX30 is required for male fertility in mice

(2017) Chun-Wei Allen Feng et al.   Scientific Reports

Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells

(2017) Samuel Rivero-Hinojosa et al.   Scientific Reports

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung 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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

YEATS2 is a selective histone crotonylation reader

(2016) Dan Zhao et al.   CELL RESEARCH

Quantitative Profiling of Combinational K27/K36 Modifications on Histone H3 Variants in Mouse Organs

(2016) Yanyan Yu et al.   JOURNAL OF PROTEOME RESEARCH

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

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

(2016) Yuanyuan Li et al.   MOLECULAR CELL

Structure of p300 in complex with acyl-CoA variants

(2016) Zuzanna Kaczmarska et al.   Nature Chemical Biology

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

Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells

(2016) Charlotte Moretti et al.   Epigenetics & Chromatin

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells

(2016) Lacey J. Luense et al.   Epigenetics & Chromatin

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

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline

(2015) Ho-Su Sin et al.   BMC BIOLOGY

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation

(2015) Matthew D. Hirschey et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of BRD4 during Mammalian Postmeiotic Sperm Development

(2015) Jessica M. Bryant et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

(2015) Xiong Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stage-specific signaling pathways during murine testis development and spermatogenesis: A pathway-based analysis to quantify developmental dynamics

(2015) Susanna H. Wegner et al.   REPRODUCTIVE TOXICOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Chromatin and Transcription Transitions of Mammalian Adult Germline Stem Cells and Spermatogenesis

(2014) Saher Sue Hammoud et al.   Cell Stem Cell

SSTY proteins co-localize with the post-meiotic sex chromatin and interact with regulators of its expression

(2014) Aurélie Comptour et al.   FEBS Journal

Genome-Scale Acetylation-Dependent Histone Eviction during Spermatogenesis

(2014) Afsaneh Goudarzi et al.   JOURNAL OF MOLECULAR BIOLOGY

Stable-isotope-labeled Histone Peptide Library for Histone Post-translational Modification and Variant Quantification by Mass Spectrometry

(2014) Shu Lin et al.   MOLECULAR & CELLULAR PROTEOMICS

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

(2014) Lunzhi Dai et al.   Nature Chemical Biology

A specific CBP/p300-dependent gene expression programme drives the metabolic remodelling in late stages of spermatogenesis

(2014) F. Boussouar et al.   Andrology

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

(2014) Xiucong Bao et al.   eLife

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

(2013) G. C. A. Taylor et al.   GENOME RESEARCH

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

(2013) Serap Erkek et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

(2013) Haiyun Gan et al.   Nature Communications

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

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

(2012) Panagis Filippakopoulos et al.   CELL

Bromodomain-dependent stage-specific male genome programming by Brdt

(2012) Jonathan Gaucher et al.   EMBO JOURNAL

Lysine Succinylation and Lysine Malonylation in Histones

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

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

(2011) Minjia Tan et al.   CELL

The double face of the histone variant H3.3

(2011) Emmanuelle Szenker 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

Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis

(2010) J. Govin et al.   GENES & DEVELOPMENT

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

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

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

Genome reprogramming during sporulation

(2009) Jerome Govin et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Mitogen-activated protein kinases in male reproductive function

(2009) Michelle W.M. Li et al.   TRENDS IN MOLECULAR MEDICINE

The Multicopy Gene Sly Represses the Sex Chromosomes in the Male Mouse Germline after Meiosis

(2009) Julie Cocquet et al.   PLOS BIOLOGY

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY