RNA m6A regulates transcription via DNA demethylation and chromatin accessibility

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

(2021) Zhenhui Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

METTL3 regulates heterochromatin in mouse embryonic stem cells

(2021) Wenqi Xu et al.   NATURE

The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity

(2021) Jiadong Liu et al.   NATURE

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

(2021) Wendan Ren et al.   Nature Communications

N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation

(2021) Yuanming Cheng et al.   CANCER CELL

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

(2021) Joo-Hyung Lee et al.   MOLECULAR CELL

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

m6A Modification in Coding and Non-coding RNAs: Roles and Therapeutic Implications in Cancer

(2020) Huilin Huang et al.   CANCER CELL

FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells

(2020) Jean A. Smith et al.   JOURNAL OF CELL BIOLOGY

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2

(2020) Yuan Li et al.   NATURE GENETICS

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

(2020) Wendan Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution

(2020) Hyun Je Kang et al.   NUCLEIC ACIDS RESEARCH

A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation

(2020) Xiao-Long Cui et al.   Nature Communications

Chromatin accessibility and the regulatory epigenome

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

Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally

(2019) Huilin Huang et al.   NATURE

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis

(2019) Daniel A. Kuppers et al.   Nature Communications

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients

(2018) De-Chen Lin et al.   GASTROENTEROLOGY

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond

(2018) Suresh Kumar et al.   Frontiers in Genetics

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease

(2017) Danuta M. Jeziorska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation

(2016) K. L. Sheaffer et al.   Cancer Prevention Research

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation

(2015) Yoshihiro Matsumura et al.   MOLECULAR CELL

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Global incidence of oesophageal cancer by histological subtype in 2012

(2014) Melina Arnold et al.   GUT

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

(2014) Schraga Schwartz et al.   Cell Reports

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction

(2013) Andrii Rudenko et al.   NEURON

UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9

(2013) Xiaoli Liu et al.   Nature Communications

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos

(2012) Toshinobu Nakamura et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites

(2012) Dheepa Balasubramanian et al.   Genome Medicine

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Transcriptional regulation by DNA methylation

(2011) Anna R. Poetsch et al.   CANCER TREATMENT REVIEWS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Making sense of chromatin states

(2011) Monya Baker   NATURE METHODS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY