Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

The methyltransferaseSetdb1is essential for meiosis and mitosis in mouse oocytes and early embryos

(2016) Angeline Eymery et al.   DEVELOPMENT

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Retrotransposons as regulators of gene expression

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

Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse

(2016) Jeesun Kim et al.   PLoS Genetics

Maternally provided LSD1/KDM1A enables the maternal-to-zygotic transition and prevents defects that manifest postnatally

(2016) Jadiel A Wasson et al.   eLife

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

(2016) Katia Ancelin et al.   eLife

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Stella preserves maternal chromosome integrity by inhibiting 5hmC-induced  H2AX accumulation

(2015) T. Nakatani et al.   EMBO REPORTS

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Maternal TET3 is dispensable for embryonic development but is required for neonatal growth

(2015) Yu-ichi Tsukada et al.   Scientific Reports

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

(2014) Miler T. Lee et al.   Annual Review of Cell and Developmental Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes

(2014) Li Shen et al.   Cell Stem Cell

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

DBTMEE: a database of transcriptome in mouse early embryos

(2014) Sung-Joon Park et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Q. Deng et al.   SCIENCE

Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

(2014) Julian R. Peat et al.   Cell Reports

Effects of Dppa3 on DNA Methylation Dynamics During Primordial Germ Cell Development in Mice1

(2013) Hiroyuki Nakashima et al.   BIOLOGY OF REPRODUCTION

The maternal to zygotic transition in mammals

(2013) Lei Li et al.   MOLECULAR ASPECTS OF MEDICINE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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(2013) Irene Cantone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Maternal control of genomic imprint maintenance

(2013) Michelle M. Denomme et al.   REPRODUCTIVE BIOMEDICINE ONLINE

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

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

(2012) Toshinobu Nakamura et al.   NATURE

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

From ancestral infectious retroviruses to bona fide cellular genes: Role of the captured syncytins in placentation

(2012) A. Dupressoir et al.   PLACENTA

Essential Role of DPPA3 for Chromatin Condensation in Mouse Oocytogenesis1

(2011) Yu-Jung Liu et al.   BIOLOGY OF REPRODUCTION

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

(2011) Mark Wossidlo et al.   Nature Communications

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Maternal control of early mouse development

(2010) L. Li et al.   DEVELOPMENT

Localization and Differential Expression of the Krüppel-Associated Box Zinc Finger Proteins 1 and 54 in Early Mouse Development

(2010) Maria Albertsen et al.   DNA AND CELL BIOLOGY

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

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

(2010) Fuchou Tang et al.   Nature Protocols

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell

Transposable elements as drivers of genomic and biological diversity in vertebrates

(2008) Astrid Böhne et al.   CHROMOSOME RESEARCH