RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

METTL3 regulates heterochromatin in mouse embryonic stem cells

(2021) Wenqi Xu et al.   NATURE

L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

(2021) Sung-Yeon Hwang et al.   Nature Communications

Increased Neural Progenitor Proliferation in a hiPSC Model of Autism Induces Replication Stress-Associated Genome Instability

(2020) Meiyan Wang et al.   Cell Stem Cell

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

(2020) Bernardo Rodriguez-Martin et al.   NATURE GENETICS

Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication

(2020) Daniel Ardeljan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells

(2020) Paolo Mita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2020) Jun Liu et al.   SCIENCE

Intron and gene size expansion during nervous system evolution

(2020) Matthew J. McCoy et al.   BMC GENOMICS

ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells

(2020) Xiaojing Liu et al.   CELL RESEARCH

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

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

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

The plasticity of DNA replication forks in response to clinically relevant genotoxic stress

(2020) Matteo Berti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Introns are mediators of cell response to starvation

(2019) Julie Parenteau et al.   NATURE

Excised linear introns regulate growth in yeast

(2019) Jeffrey T. Morgan et al.   NATURE

RNA: Nuclear Glue for Folding the Genome

(2019) Ryu-Suke Nozawa et al.   TRENDS IN CELL BIOLOGY

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

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

(2019) Huilin Huang et al.   NATURE

LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation

(2019) Matthew Simon et al.   Cell Metabolism

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

(2019) Diane A. Flasch et al.   CELL

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

(2019) Tania Sultana et al.   MOLECULAR CELL

The RNA N6-methyladenosine modification landscape of human fetal tissues

(2019) Shan Xiao et al.   NATURE CELL BIOLOGY

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals

(2019) Boxun Zhao et al.   PLoS Genetics

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression

(2019) Erdem Sendinc et al.   MOLECULAR CELL

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

(2019) Yingyao Zhou et al.   Nature Communications

Host–transposon interactions: conflict, cooperation, and cooption

(2019) Rachel L Cosby et al.   GENES & DEVELOPMENT

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Transposable elements in human genetic disease

(2019) Lindsay M. Payer et al.   NATURE REVIEWS GENETICS

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders

(2018) Jasmine Jacob-Hirsch et al.   CELL RESEARCH

The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes

(2018) Luisa Robbez-Masson et al.   GENOME RESEARCH

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

(2018) Jing Wen et al.   MOLECULAR CELL

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

Biallelic loss of human CTNNA2, encoding αN-catenin, leads to ARP2/3 complex overactivity and disordered cortical neuronal migration

(2018) Ashleigh E. Schaffer et al.   NATURE GENETICS

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

(2018) Xiaoji Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early life experience drives structural variation of neural genomes in mice

(2018) Tracy A. Bedrosian et al.   SCIENCE

Chemical Modifications in the Life of an mRNA Transcript

(2018) Sigrid Nachtergaele et al.   Annual Review of Genetics

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

(2018) Jan Attig et al.   CELL

Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s

(2018) Zbigniew Warkocki et al.   CELL

The human microglial HMC3 cell line: where do we stand? A systematic literature review

(2018) Cinzia Dello Russo et al.   Journal of Neuroinflammation

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

(2018) Yoav Lubelsky et al.   NATURE

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

(2018) Shinichiro Akichika et al.   SCIENCE

Microglia in Alzheimer’s disease

(2017) Heela Sarlus et al.   JOURNAL OF CLINICAL INVESTIGATION

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mobile DNA in Health and Disease

(2017) Haig H. Kazazian et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

m6aViewer: software for the detection, analysis, and visualization of N 6 -methyladenosine peaks from m 6 A-seq/ME-RIP sequencing data

(2017) Agne Antanaviciute et al.   RNA

L1 Mosaicism in Mammals: Extent, Effects, and Evolution

(2017) Geoffrey J. Faulkner et al.   TRENDS IN GENETICS

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

(2017) Ian A Roundtree et al.   eLife

The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins

(2016) M. Norman et al.   BIOCHEMICAL JOURNAL

Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

(2016) Pei-Chi Wei et al.   CELL

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

RNA as a fundamental component of interphase chromosomes: could repeats prove key?

(2016) Lisa L Hall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

New insights on the role of microglia in synaptic pruning in health and disease

(2016) Soyon Hong et al.   CURRENT OPINION IN NEUROBIOLOGY

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

An RB-EZH2 Complex Mediates Silencing of Repetitive DNA Sequences

(2016) Charles A. Ishak et al.   MOLECULAR CELL

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

L1-associated genomic regions are deleted in somatic cells of the healthy human brain

(2016) Jennifer A Erwin et al.   NATURE NEUROSCIENCE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

The Fanconi anaemia pathway: new players and new functions

(2016) Raphael Ceccaldi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes

(2016) Tobias Penzkofer et al.   NUCLEIC ACIDS RESEARCH

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

(2016) Claude Philippe et al.   eLife

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

(2015) Caroline Rivers et al.   BMC BIOLOGY

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Loss of δ-catenin function in severe autism

(2015) Tychele N. Turner et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

(2015) Bastian Linder et al.   NATURE METHODS

Gene Length Matters in Neurons

(2015) Mark J. Zylka et al.   NEURON

L1 Retrotransposons and Somatic Mosaicism in the Brain

(2014) Sandra R. Richardson et al.   Annual Review of Genetics

Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes

(2014) Lisa L. Hall et al.   CELL

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission

(2014) T. Karayannis et al.   NATURE

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain

(2014) Chao Xu et al.   Nature Chemical Biology

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

Gephyrin: a master regulator of neuronal function?

(2014) Shiva K. Tyagarajan et al.   NATURE REVIEWS NEUROSCIENCE

Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia

(2014) Miki Bundo et al.   NEURON

A critical analysis of codon optimization in human therapeutics

(2014) Vincent P. Mauro et al.   TRENDS IN MOLECULAR MEDICINE

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

(2014) Schraga Schwartz et al.   Cell Reports

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

(2013) N. A. Kearns et al.   DEVELOPMENT

Multiple Epigenetic Mechanisms and the piRNA Pathway Enforce LINE1 Silencing during Adult Spermatogenesis

(2013) Monica Di Giacomo et al.   MOLECULAR CELL

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair

(2013) L. Wan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the evolution of mouse LINE-1 in the genomic era

(2013) Akash Sookdeo et al.   Mobile DNA

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs)

(2013) Brett S Abrahams et al.   Molecular Autism

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Kate D. Meyer et al.   CELL

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2012) Dan Dominissini et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

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

(2011) Guifang Jia et al.   Nature Chemical Biology

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

The Angelman Syndrome Protein Ube3A Regulates Synapse Development by Ubiquitinating Arc

(2010) Paul L. Greer et al.   CELL

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

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

The RNA Polymerase Dictates ORF1 Requirement and Timing of LINE and SINE Retrotransposition

(2009) Emily N. Kroutter et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY