The epitranscriptome in stem cell biology and neural development

Dynamic landscape and evolution of m6A methylation in human

(2020) Hui Zhang et al.   NUCLEIC ACIDS RESEARCH

YTHDF2 destabilizes m6A-modified neural-specific RNAs to restrain differentiation in induced pluripotent stem cells

(2020) Adam M. Heck et al.   RNA

Limits in the detection of m6A changes using MeRIP/m6A-seq

(2020) Alexa B. R. McIntyre et al.   Scientific Reports

A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA

(2020) Sara Zaccara et al.   CELL

Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase

(2020) Christopher Wilson et al.   NATURE BIOTECHNOLOGY

m6A methylation controls pluripotency of porcine induced pluripotent stem cells by targeting SOCS3/JAK2/STAT3 pathway in a YTHDF1/YTHDF2-orchestrated manner

(2019) Ruifan Wu et al.   Cell Death & Disease

Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution

(2019) Vahid Khoddami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FTO controls reversible m6Am RNA methylation during snRNA biogenesis

(2019) Jan Mauer et al.   Nature Chemical Biology

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

(2019) Huilin Huang et al.   NATURE

PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly

(2019) Ranad Shaheen et al.   HUMAN GENETICS

Special Issue on Regulating the Central Dogma

(2019) Chuan He   BIOCHEMISTRY

Genome-wide identification of mRNA 5-methylcytosine in mammals

(2019) Tao Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

m6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2

(2019) Junchen Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling

(2019) Miguel Angel Garcia-Campos et al.   CELL

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression

(2019) Erdem Sendinc et al.   MOLECULAR CELL

The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112

(2019) Nhan van Tran et al.   NUCLEIC ACIDS RESEARCH

Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation

(2019) Abdulrahim A. Sajini et al.   Nature Communications

FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export

(2019) Brittany M. Edens et al.   Cell Reports

Interplay Between N6-Methyladenosine (m6A) and Non-coding RNAs in Cell Development and Cancer

(2019) Francesco Fazi et al.   Frontiers in Cell and Developmental Biology

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay

(2019) Ying Yang et al.   MOLECULAR CELL

mRNA structure determines modification by pseudouridine synthase 1

(2019) Thomas M. Carlile et al.   Nature Chemical Biology

Bi-allelic Variants in METTL5 Cause Autosomal-Recessive Intellectual Disability and Microcephaly

(2019) Elodie M. Richard et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dynamic effects of Fto in regulating the proliferation and differentiation of adult neural stem cells of mice

(2019) Yuhang Cao et al.   HUMAN MOLECULAR GENETICS

The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine–containing mRNAs

(2019) Phillip J. Hsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues

(2019) Jun’e Liu et al.   MOLECULAR CELL

Antibody cross-reactivity accounts for widespread appearance of m1A in 5’UTRs

(2019) Anya V. Grozhik et al.   Nature Communications

The m6A epitranscriptome: transcriptome plasticity in brain development and function

(2019) Ido Livneh et al.   NATURE REVIEWS NEUROSCIENCE

Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes

(2019) Casslynn W. Q. Koh et al.   Nature Communications

FTO is involved in Alzheimer's disease by targeting TSC1-mTOR-Tau signaling

(2018) Huajie Li et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d

(2018) Philip Knuckles et al.   GENES & DEVELOPMENT

Epigenetics and epitranscriptomics in temporal patterning of cortical neural progenitor competence

(2018) Ki-Jun Yoon et al.   JOURNAL OF CELL BIOLOGY

Zc3h13 Regulates Nuclear RNA m 6 A Methylation and Mouse Embryonic Stem Cell Self-Renewal

(2018) Jing Wen et al.   MOLECULAR CELL

N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications

(2018) Yang Wang et al.   NATURE NEUROSCIENCE

Epitranscriptomic m 6 A Regulation of Axon Regeneration in the Adult Mammalian Nervous System

(2018) Yi-Lan Weng et al.   NEURON

Reading m 6 A in the Transcriptome: m 6 A-Binding Proteins

(2018) Deepak P. Patil et al.   TRENDS IN CELL BIOLOGY

METTL3-mediated m6A modification is required for cerebellar development

(2018) Chen-Xin Wang et al.   PLOS BIOLOGY

Coupling Transcription and Translation via the Epitranscriptomic m6A Mark

(2018) Kun Wang et al.   BIOCHEMISTRY

The Obesity Related Gene, FTO, Interacts with APOE, and is Associated with Alzheimer's Disease Risk: A Prospective Cohort Study

(2018) Lina Keller et al.   JOURNAL OF ALZHEIMERS DISEASE

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development

(2018) Mateusz Mendel et al.   MOLECULAR CELL

Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm

(2018) Jiangbo Wei et al.   MOLECULAR CELL

The Role of m6A/m-RNA Methylation in Stress Response Regulation

(2018) Mareen Engel et al.   NEURON

M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map

(2018) Schraga Schwartz   RNA

Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior

(2018) Arjan P.M. de Brouwer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The m6A Writer: Rise of a Machine for Growing Tasks

(2018) Dario L. Balacco et al.   BIOCHEMISTRY

Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase

(2018) Hanxiao Sun et al.   CELL RESEARCH

m6A facilitates hippocampus-dependent learning and memory through YTHDF1

(2018) Hailing Shi et al.   NATURE

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

(2017) Carine Legrand et al.   GENOME RESEARCH

Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis

(2017) Liping Li et al.   HUMAN MOLECULAR GENETICS

NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation

(2017) Qiu Li et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein–RNA Interactome

(2017) A. Emilia Arguello et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Pseudouridine and N 6 -methyladenosine modifications weaken PUF protein/RNA interactions

(2017) Pavanapuresan P. Vaidyanathan et al.   RNA

m 6 A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells

(2017) Qi Cui et al.   Cell Reports

Region-specific RNA m 6 A methylation represents a new layer of control in the gene regulatory network in the mouse brain

(2017) Mengqi Chang et al.   Open Biology

Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility

(2017) Joana V. Flores et al.   Stem Cell Reports

ALKBHs-facilitated RNA modifications and de-modifications

(2016) Endalkachew A. Alemu et al.   DNA REPAIR

A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition

(2016) Ranad Shaheen et al.   HUMAN GENETICS

Experience-Dependent Accumulation of N 6 -Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

(2016) Jocelyn Widagdo et al.   JOURNAL OF NEUROSCIENCE

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA

(2016) Chuanzhao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Hypoxia-inducible factors regulate pluripotency factor expression by ZNF217- and ALKBH5-mediated modulation of RNA methylation in breast cancer cells

(2016) Chuanzhao Zhang et al.   Oncotarget

m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency

(2015) Tong Chen et al.   Cell Stem Cell

Coordination of m 6 A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming

(2015) Francesca Aguilo et al.   Cell Stem Cell

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

Dysregulation and restoration of translational homeostasis in fragile X syndrome

(2015) Joel D. Richter et al.   NATURE REVIEWS NEUROSCIENCE

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Fate by RNA methylation: m6A steers stem cell pluripotency

(2015) Boxuan Zhao et al.   GENOME BIOLOGY

Pseudouridine: Still mysterious, but never a fake (uridine)!

(2015) Felix Spenkuch et al.   RNA Biology

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

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

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

Tet-Mediated Formation of 5-Hydroxymethylcytosine in RNA

(2014) Lijuan Fu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

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

(2014) Schraga Schwartz et al.   Cell Reports

Identification of Wilms' Tumor 1-associating Protein Complex and Its Role in Alternative Splicing and the Cell Cycle

(2013) Keiko Horiuchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry

(2013) Martin E Hess et al.   NATURE NEUROSCIENCE

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing

(2013) Dan Dominissini et al.   Nature Protocols

Association between obesity-related geneFTOand ADHD

(2013) Zia Choudhry et al.   Obesity

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Mutations in NSUN2 Cause Autosomal- Recessive Intellectual Disability

(2012) Lia Abbasi-Moheb et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Neuronal circuitry mechanism regulating adult quiescent neural stem-cell fate decision

(2012) Juan Song et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   CELL

Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond

(2011) Junjie U. Guo et al.   CELL CYCLE

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Adult Neurogenesis in the Mammalian Brain: Significant Answers and Significant Questions

(2011) Guo-li Ming et al.   NEURON

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

The Fat Mass and Obesity Associated Gene FTO Functions in the Brain to Regulate Postnatal Growth in Mice

(2010) Xue Gao et al.   PLoS One

5-methylcytosine in RNA: detection, enzymatic formation and biological functions

(2009) Yuri Motorin et al.   NUCLEIC ACIDS RESEARCH

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL