Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation

Mitochondrial complex III is essential for suppressive function of regulatory T cells

(2019) Samuel E. Weinberg et al.   NATURE

A Practical Guide to the Measurement and Analysis of DNA Methylation

(2019) Benjamin D Singer   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

(2018) X. Shawn Liu et al.   CELL

CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog

(2018) Ganesh V. Pusapati et al.   DEVELOPMENTAL CELL

DNA methylation regulates the neonatal CD4+ T-cell response to pneumonia in mice

(2018) Sharon McGrath-Morrow et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer

(2018) Srinivas R. Viswanathan et al.   NATURE GENETICS

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

(2018) Glòria Mas et al.   NATURE GENETICS

TET2 coactivates gene expression through demethylation of enhancers

(2018) Lu Wang et al.   Science Advances

Histone H3K4 methylation-dependent and -independent functions of Set1A/COMPASS in embryonic stem cell self-renewal and differentiation

(2017) Christie C. Sze et al.   GENES & DEVELOPMENT

SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

(2017) Kaixiang Cao et al.   GENES & DEVELOPMENT

Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

(2017) Deqing Hu et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

(2017) Ryan Rickels et al.   NATURE GENETICS

Haploinsufficiency of KMT2B , Encoding the Lysine-Specific Histone Methyltransferase 2B, Results in Early-Onset Generalized Dystonia

(2016) Michael Zech et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Is H3K4me3 instructive for transcription activation?

(2016) Françoise S. Howe et al.   BIOESSAYS

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS

(2016) Ryan Rickels et al.   MOLECULAR CELL

Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia

(2016) Esther Meyer et al.   NATURE GENETICS

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Epigenetic balance of gene expression by Polycomb and COMPASS families

(2016) Andrea Piunti et al.   SCIENCE

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Chromatin signatures of cancer

(2015) Marc A. Morgan et al.   GENES & DEVELOPMENT

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

(2015) Liv M.I. Austenaa et al.   MOLECULAR CELL

Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells

(2015) Zhiguang Li et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

(2013) D. Hu et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells

(2013) Deqing Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Two mammalian MAGOH genes contribute to exon junction complex composition and nonsense-mediated decay

(2013) Kusum K Singh et al.   RNA Biology

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4

(2012) H.-M. Herz et al.   GENES & DEVELOPMENT

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

(2012) Thanasis Margaritis et al.   PLoS Genetics

The COMPASS Family of H3K4 Methylases in Drosophila

(2011) M. Mohan et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin

(2009) Courtney M. Tate et al.   FEBS Journal

The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis

(2009) Stefan Glaser et al.   Epigenetics & Chromatin

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

(2008) M. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY