Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate

(2019) Abhishek A. Chakraborty et al.   SCIENCE

Cancer-associated 2-oxoglutarate analogues modify histone methylation by inhibiting histone lysine demethylases

(2018) Tuomas Laukka et al.   JOURNAL OF MOLECULAR BIOLOGY

The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity

(2018) May Levin et al.   Oncotarget

Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases

(2017) Zhenlin Yang et al.   PLANT CELL

Redox signaling during hypoxia in mammalian cells

(2017) Kimberly A. Smith et al.   Redox Biology

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

KDM2 Family Members are Regulated by HIF-1 in Hypoxia

(2017) Michael Batie et al.   Cells

Succinate, an intermediate in metabolism, signal transduction, ROS, hypoxia, and tumorigenesis

(2016) Laszlo Tretter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

(2016) Peggy Prickaerts et al.   Epigenetics & Chromatin

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

(2016) Michiel E. Adriaens et al.   Epigenetics & Chromatin

Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition

(2016) Julianty Frost et al.   Nature Communications

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

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Evolution and conservation of JmjC domain proteins in the green lineage

(2015) Yong Huang et al.   MOLECULAR GENETICS AND GENOMICS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Chromatin and oxygen sensing in the context of JmjC histone demethylases

(2014) Alena Shmakova et al.   BIOCHEMICAL JOURNAL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Enzymatic assay for quantitative analysis of (d)-2-hydroxyglutarate

(2012) Jörg Balss et al.   ACTA NEUROPATHOLOGICA

Investigations on the oxygen dependence of a 2-oxoglutarate histone demethylase

(2012) Elena M. Sánchez-Fernández et al.   BIOCHEMICAL JOURNAL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Chromatin as an oxygen sensor and active player in the hypoxia response

(2011) Andrew Melvin et al.   CELLULAR SIGNALLING

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Crystal structure of the catalytic core ofSaccharomyces cerevesiaehistone demethylase Rph1: insights into the substrate specificity and catalytic mechanism

(2010) Yuanyuan Chang et al.   BIOCHEMICAL JOURNAL

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction

(2010) Amaya Ortiz-Barahona et al.   NUCLEIC ACIDS RESEARCH

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

(2009) Yair Benita et al.   NUCLEIC ACIDS RESEARCH

Regulation of gene expression by hypoxia

(2008) Niall Steven Kenneth et al.   BIOCHEMICAL JOURNAL

Regulation of Jumonji-domain-containing histone demethylases by hypoxia-inducible factor (HIF)-1α

(2008) Patrick J. Pollard et al.   BIOCHEMICAL JOURNAL

Oxygen Sensing by Metazoans: The Central Role of the HIF Hydroxylase Pathway

(2008) William G. Kaelin et al.   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY