Evolutionary epigenomic analyses in mammalian early embryos reveal species-specific innovations and conserved principles of imprinting

DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes

(2020) Elena Ivanova et al.   Clinical Epigenetics

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

(2020) Yang Zhou et al.   BMC BIOLOGY

Maternal H3K27me3-dependent autosomal and X chromosome imprinting

(2020) Zhiyuan Chen et al.   NATURE REVIEWS GENETICS

Dux-Mediated Corrections of Aberrant H3K9ac during 2-Cell Genome Activation Optimize Efficiency of Somatic Cell Nuclear Transfer

(2020) Guang Yang et al.   Cell Stem Cell

NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

(2020) Kenjiro Shirane et al.   NATURE GENETICS

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

(2020) Saikat Bhattacharya et al.   Epigenetics & Chromatin

Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation

(2020) Michelle M. Halstead et al.   Nature Communications

Rebooting the Epigenomes during Mammalian Early Embryogenesis

(2020) Weikun Xia et al.   Stem Cell Reports

Maternal-biased H3K27me3 correlates with paternal-specific gene expression in the human morula

(2019) Wenhao Zhang et al.   GENES & DEVELOPMENT

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

(2019) Qianhua Xu et al.   NATURE GENETICS

Methylome Dynamics of Bovine Gametes and in vivo Early Embryos

(2019) Jingyue Ellie Duan et al.   Frontiers in Genetics

No imprinted XIST expression in pigs: biallelic XIST expression in early embryos and random X inactivation in placentas

(2019) Huiying Zou et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Roles and regulation of histone methylation in animal development

(2019) Ashwini Jambhekar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Resetting histone modifications during human parental-to-zygotic transition

(2019) Weikun Xia et al.   SCIENCE

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(2019) Daniel N. Weinberg et al.   NATURE

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The role and mechanisms of DNA methylation in the oocyte

(2019) Gintarė Sendžikaitė et al.   Essays in Biochemistry

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos

(2019) Zhenhai Du et al.   MOLECULAR CELL

Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency

(2019) Yunlong Xiang et al.   NATURE GENETICS

Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells

(2019) Zhiyuan Chen et al.   Science Advances

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts

(2018) Yanina Soledad Bogliotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

(2018) Julie Brind’Amour et al.   Nature Communications

Maternal Eed knockout causes loss of H3K27me3 imprinting and random X inactivation in the extraembryonic cells

(2018) Azusa Inoue et al.   GENES & DEVELOPMENT

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Maternal H3K27me3 controls DNA methylation-independent imprinting

(2017) Azusa Inoue et al.   NATURE

Single-cell DNA methylome sequencing of human preimplantation embryos

(2017) Ping Zhu et al.   NATURE GENETICS

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

(2017) Yu Zhang et al.   NATURE GENETICS

Characterization of X-Chromosome Gene Expression in Bovine Blastocysts Derived by In vitro Fertilization and Somatic Cell Nuclear Transfer

(2017) Byungkuk Min et al.   Frontiers in Genetics

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals

(2016) Hui Zheng et al.   MOLECULAR CELL

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

(2016) Xiaoyu Liu et al.   NATURE

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Parallel evolution of male germline epigenetic poising and somatic development in animals

(2016) Bluma J Lesch et al.   NATURE GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Impairment of Preimplantation Porcine Embryo Development by Histone Demethylase KDM5B Knockdown Through Disturbance of Bivalent H3K4me3-H3K27me3 Modifications1

(2015) Jiaojiao Huang et al.   BIOLOGY OF REPRODUCTION

Parthenogenetic haploid embryonic stem cells efficiently support mouse generation by oocyte injection

(2015) Cuiqing Zhong et al.   CELL RESEARCH

Birth of fertile bimaternal offspring following intracytoplasmic injection of parthenogenetic haploid embryonic stem cells

(2015) Zhikun Li et al.   CELL RESEARCH

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

(2015) Neil P. Blackledge et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-Wide Dynamic Profiling of Histone Methylation during Nuclear Transfer-Mediated Porcine Somatic Cell Reprogramming

(2015) Zubing Cao et al.   PLoS One

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

The developmental hourglass model: a predictor of the basic body plan?

(2014) N. Irie et al.   DEVELOPMENT

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

TELP, a sensitive and versatile library construction method for next-generation sequencing

(2014) Xu Peng et al.   NUCLEIC ACIDS RESEARCH

Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease

(2014) Michelle D. Johnson et al.   PLoS Genetics

Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

(2014) Hiroaki Okae et al.   PLoS Genetics

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

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

(2012) Wei Xie et al.   CELL

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

In vitro production of porcine embryos: current status, future perspectives and alternative applications

(2011) Thanh Quang DANG-NGUYEN et al.   ANIMAL SCIENCE JOURNAL

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

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

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Yufeng Li et al.   CELL RESEARCH

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation

(2011) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

(2011) Frank W. Schmitges et al.   MOLECULAR CELL

MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing

(2010) Claudia V. Andreu-Vieyra et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Polycomb gene expression and histone H3 lysine 27 trimethylation changes during bovine preimplantation development

(2008) Pablo J Ross et al.   REPRODUCTION