Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo

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

Precise allele-specific genome editing by spatiotemporal control of CRISPR-Cas9 via pronuclear transplantation

(2020) Yanhe Li et al.   Nature Communications

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

(2020) Wanqing Shao et al.   GENOME RESEARCH

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Reprogramming during Mammalian Development

(2019) Yang Zeng et al.   Genes

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

(2018) Chenfei Wang et al.   NATURE CELL BIOLOGY

Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

(2018) Qianhua Xu et al.   TRENDS IN CELL BIOLOGY

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

Characterization and dynamics of pericentromere-associated domains in mice

(2015) Patrick J. Wijchers et al.   GENOME RESEARCH

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse

(2015) Tomas Babak et al.   NATURE GENETICS

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

Understanding the relationship between DNA methylation and histone lysine methylation

(2014) Nathan R. Rose et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

MetaImprint: an information repository of mammalian imprinted genes

(2014) Y. Wei et al.   DEVELOPMENT

The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals

(2014) R. Duffie et al.   GENES & DEVELOPMENT

Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis

(2014) Adam Burton et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

(2014) D. Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

(2013) Xiaoli Liu et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

(2012) Charlotte Proudhon et al.   MOLECULAR CELL

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

(2012) Toshinobu Nakamura et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

(2012) Scott B Rothbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Trim28 Is Required for Epigenetic Stability During Mouse Oocyte to Embryo Transition

(2012) D. M. Messerschmidt et al.   SCIENCE

Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming

(2011) Yufeng Li et al.   CELL RESEARCH

Zinc Finger Protein ZFP57 Requires Its Co-factor to Recruit DNA Methyltransferases and Maintains DNA Methylation Imprint in Embryonic Stem Cells via Its Transcriptional Repression Domain

(2011) Xiaopan Zuo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

WAMIDEX: A web atlas of murine genomic imprinting and differential expression

(2010) Reiner Schulz et al.   Epigenetics

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity

(2008) Kevin B Dong et al.   EMBO JOURNAL

Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development

(2008) R. Hirasawa et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY