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

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

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

(2020) Jun Liu et al.   SCIENCE

SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States

(2020) Kaixin Wu et al.   Cell Reports

A cell in hand is worth two in the embryo: recent advances in 2-cell like cell reprogramming

(2020) Ane Iturbide et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The molecular and cellular features of 2-cell-like cells: a reference guide

(2020) Marion Genet et al.   DEVELOPMENT

YTHDF2/3 Are Required for Somatic Reprogramming through Different RNA Deadenylation Pathways

(2020) Jiadong Liu et al.   Cell Reports

Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development

(2019) Zhiyuan Chen et al.   NATURE GENETICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nuclear Exosome Targeting Complex Core Factor Zcchc8 Regulates the Degradation of LINE1 RNA in Early Embryos and Embryonic Stem Cells

(2019) You Wu et al.   Cell Reports

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

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

(2018) Ying Yang et al.   CELL RESEARCH

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

(2018) Seth D. Kasowitz et al.   PLoS Genetics

GoldCLIP: Gel-omitted Ligation-dependent CLIP

(2018) Jiaqi Gu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

m6A facilitates hippocampus-dependent learning and memory through YTHDF1

(2018) Hailing Shi et al.   NATURE

RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation

(2018) Yuan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence

(2017) Ivayla Ivanova et al.   MOLECULAR CELL

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

From the stem of the placental tree: trophoblast stem cells and their progeny

(2016) Paulina Anna Latos et al.   DEVELOPMENT

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ying Jin et al.   BIOINFORMATICS

A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1

(2015) Chongyuan Wang et al.   NUCLEIC ACIDS RESEARCH

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

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

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

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

(2014) Chao Xu et al.   Nature Chemical Biology

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain

(2014) S. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

Establishment of totipotency does not depend on Oct4A

(2013) Guangming Wu et al.   NATURE CELL BIOLOGY

The octamer is the major form of CENP-A nucleosomes at human centromeres

(2013) Dan Hasson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

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

(2012) Dan Dominissini et al.   NATURE

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs

(2012) Jiekai Chen et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

RNA Elimination Machinery Targeting Meiotic mRNAs Promotes Facultative Heterochromatin Formation

(2011) M. Zofall et al.   SCIENCE

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

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5

(2008) Ray Kit Ng et al.   NATURE CELL BIOLOGY