Maternal factor NELFA drives a 2C-like state in mouse embryonic stem cells

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

(2019) Mélanie Eckersley-Maslin et al.   GENES & DEVELOPMENT

DPPA2 and DPPA4 are necessary to establish a 2C‐like state in mouse embryonic stem cells

(2019) Alberto De Iaco et al.   EMBO REPORTS

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

(2019) Zhiyuan Chen et al.   NATURE GENETICS

Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells

(2019) Xudong Fu et al.   NATURE CELL BIOLOGY

Proteomic profiling of barley spent grains guides enzymatic solubilization of the remaining proteins

(2018) Xuezhi Bi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming

(2018) Ting Zhao et al.   Cell Stem Cell

Programmed DNA Breaks Activate the Germline Genome in Caenorhabditis elegans

(2018) Matthew M. Wong et al.   DEVELOPMENTAL CELL

Establishment of mouse expanded potential stem cells

(2017) Jian Yang et al.   NATURE

The impact of cellular metabolism on chromatin dynamics and epigenetics

(2017) Michael A. Reid et al.   NATURE CELL BIOLOGY

A molecular roadmap for the emergence of early-embryonic-like cells in culture

(2017) Diego Rodriguez-Terrones et al.   NATURE GENETICS

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco 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

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Deficiency of microRNAmiR-34aexpands cell fate potential in pluripotent stem cells

(2017) Yong Jin Choi et al.   SCIENCE

Mammalian zygotic genome activation

(2017) Petr Svoboda   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Stat3 promotes mitochondrial transcription and oxidative respiration during maintenance and induction of naive pluripotency

(2016) Elena Carbognin et al.   EMBO JOURNAL

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

(2016) Xiaoyu Liu et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation

(2016) Katia Ancelin et al.   eLife

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism

(2015) Samantha J. Mentch et al.   Cell Metabolism

Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells

(2015) Tomohiko Akiyama et al.   DNA RESEARCH

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

(2015) Yuki Hatanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Core Pluripotency Factors Directly Regulate Metabolism in Embryonic Stem Cell to Maintain Pluripotency

(2015) Hyunsoo Kim et al.   STEM CELLS

Reprogramming the genome to totipotency in mouse embryos

(2015) Li-quan Zhou et al.   TRENDS IN CELL BIOLOGY

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

(2013) Masashi Yamaji et al.   Cell Stem Cell

Towards an understanding of the regulatory mechanisms of totipotency

(2013) Takashi Ishiuchi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation

(2013) Nils Grabole et al.   EMBO REPORTS

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells

(2013) Irina A Maksakova et al.   Epigenetics & Chromatin

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling

(2011) Richard P. Koche et al.   Cell Stem Cell

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A

(2011) Todd S. Macfarlan et al.   GENES & DEVELOPMENT

Zscan4 regulates telomere elongation and genomic stability in ES cells

(2010) Michal Zalzman et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates

(2010) Ziyang Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Role of Fatty Acids in Energy Provision During Oocyte Maturation and Early Embryo Development

(2009) RG Sturmey et al.   REPRODUCTION IN DOMESTIC ANIMALS

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE