4.8 Article

RNA m6A regulates transcription via DNA demethylation and chromatin accessibility

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma

Yiyi Xi et al.

Summary: This study examines aberrant DNA methylations as potential markers for diagnosis and prognosis of esophageal squamous-cell carcinoma (ESCC). Various differentially methylated CpG sites were identified, and diagnostic and prognostic panels were developed.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

Article Multidisciplinary Sciences

m6A RNA methylation regulates the fate of endogenous retroviruses

Tomasz Chelmicki et al.

Summary: Research indicates that m(6)A RNA methylation can restrict ERVs, maintaining cellular integrity by reducing the half-life of IAP mRNA to clear reactive ERV-derived RNA species.

NATURE (2021)

Article Biochemistry & Molecular Biology

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

Hyun Je Kang et al.

Summary: R-loops are three-stranded RNA-DNA structures that can cause genomic instability and malignant diseases when accumulated. TonEBP can recognize and bind to R-loops, recruiting METTL3 for m6A RNA methylation, providing a new pathway for R-loop resolution.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

Zhenhui Zhong et al.

Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Multidisciplinary Sciences

METTL3 regulates heterochromatin in mouse embryonic stem cells

Wenqi Xu et al.

Summary: METTL3 regulates mouse embryonic stem-cell heterochromatin, critical for silencing retroviral elements and mammalian development. Through m(6)A methylation, METTL3 modulates integrity of IAP heterochromatin.

NATURE (2021)

Article Multidisciplinary Sciences

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

Jiadong Liu et al.

Summary: The study reveals that the m(6)A RNA modification and YTHDC1 play essential roles in regulating retrotransposons and cellular reprogramming during early mouse embryonic development.

NATURE (2021)

Article Multidisciplinary Sciences

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

Wendan Ren et al.

Summary: The study reveals that DNA methyltransferase DNMT1 acts as a reader for histone H4K20 trimethylation through its BAH1 domain, ensuring optimal maintenance of DNA methylation at repetitive LINE-1 elements.

NATURE COMMUNICATIONS (2021)

Article Oncology

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

Yuanming Cheng et al.

Summary: The study revealed the crucial role of m(6)A in myeloid leukemia, where it maintains cell survival and the undifferentiated state necessary for leukemia maintenance through the formation of nuclear YTHDC1-m(6)A condensates.

CANCER CELL (2021)

Article Biochemistry & Molecular Biology

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

Joo-Hyung Lee et al.

Summary: The study reveals the heavy but selective deposition of m6A on nascent RNAs produced by transcription regulatory elements, and shows that m6A-eRNAs mark highly active enhancers by recruiting YTHDC1 and promoting condensate formation. This mechanism plays broad roles in enhancer activation and gene transcriptional control.

MOLECULAR CELL (2021)

Article Genetics & Heredity

N-6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

Abdulkadir Abakir et al.

NATURE GENETICS (2020)

Letter Biotechnology & Applied Microbiology

Visualizing and interpreting cancer genomics data via the Xena platform

Mary J. Goldman et al.

NATURE BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

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

Wendan Ren et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Biochemistry & Molecular Biology

Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof

Erik W. Martin et al.

EMERGING TOPICS IN LIFE SCIENCES (2020)

Article Multidisciplinary Sciences

m6A enhances the phase separation potential of mRNA

Ryan J. Ries et al.

NATURE (2019)

Article Multidisciplinary Sciences

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

Daniel A. Kuppers et al.

NATURE COMMUNICATIONS (2019)

Article Genetics & Heredity

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

Khelifa Arab et al.

NATURE GENETICS (2019)

Review Genetics & Heredity

Chromatin accessibility and the regulatory epigenome

Sandy L. Klemm et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Gastroenterology & Hepatology

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

De-Chen Lin et al.

GASTROENTEROLOGY (2018)

Review Genetics & Heredity

Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond

Suresh Kumar et al.

FRONTIERS IN GENETICS (2018)

Review Genetics & Heredity

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

Xiaoji Wu et al.

NATURE REVIEWS GENETICS (2017)

Article Biochemistry & Molecular Biology

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

Raghu R. Edupuganti et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Multidisciplinary Sciences

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

Danuta M. Jeziorska et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemistry & Molecular Biology

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

Raghu R. Edupuganti et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Biochemical Research Methods

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

Xiaodong Cui et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

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

Yongseok Park et al.

BIOINFORMATICS (2016)

Article Oncology

DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation

Karyn L. Sheaffer et al.

CANCER PREVENTION RESEARCH (2016)

Article Biochemistry & Molecular Biology

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

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Sambamba: fast processing of NGS alignment formats

Artem Tarasov et al.

BIOINFORMATICS (2015)

Article Gastroenterology & Hepatology

Global incidence of oesophageal cancer by histological subtype in 2012

Melina Arnold et al.

Article Cell & Tissue Engineering

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

Pedro J. Batista et al.

CELL STEM CELL (2014)

Review Genetics & Heredity

Gene expression regulation mediated through reversible m6A RNA methylation

Ye Fu et al.

NATURE REVIEWS GENETICS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Review Biochemistry & Molecular Biology

Transcriptional Regulation and Its Misregulation in Disease

Tong Ihn Lee et al.

Article Biochemical Research Methods

Site identification in high-throughput RNA-protein interaction data

Philip J. Uren et al.

BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

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

Caryn S. Ross-Innes et al.

NATURE (2012)

Article Multidisciplinary Sciences

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

Toshinobu Nakamura et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

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

Karen Adelman et al.

NATURE REVIEWS GENETICS (2012)

Article Biotechnology & Applied Microbiology

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

Altuna Akalin et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

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

Felix Krueger et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

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

Bo Li et al.

BMC BIOINFORMATICS (2011)

Review Oncology

Transcriptional regulation by DNA methylation

Anna R. Poetsch et al.

CANCER TREATMENT REVIEWS (2011)

Review Cell Biology

Regulation of chromatin by histone modifications

Andrew J. Bannister et al.

CELL RESEARCH (2011)

Editorial Material Biochemical Research Methods

Making sense of chromatin states

Monya Baker

NATURE METHODS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Review Genetics & Heredity

Linking DNA methylation and histone modification: patterns and paradigms

Howard Cedar et al.

NATURE REVIEWS GENETICS (2009)

Review Genetics & Heredity

DNA methylation landscapes: provocative insights from epigenomics

Miho M. Suzuki et al.

NATURE REVIEWS GENETICS (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Multidisciplinary Sciences

DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

Steen K. T. Ooi et al.

NATURE (2007)

Review Biochemistry & Molecular Biology

DNA methylation and chromatin - unraveling the tangled web

KD Robertson

ONCOGENE (2002)

Article Cell Biology

Histone modifications in transcriptional regulation

SL Berger

CURRENT OPINION IN GENETICS & DEVELOPMENT (2002)