Retention of paternal DNA methylome in the developing zebrafish germline

Abundance of Early Embryonic Primordial Germ Cells Promotes Zebrafish Female Differentiation as Revealed by Lifetime Labeling of Germline

(2019) Ding Ye et al.   MARINE BIOTECHNOLOGY

Zebrafish preserve global germline DNA methylation while sex-linked rDNA is amplified and demethylated during feminisation

(2019) Oscar Ortega-Recalde et al.   Nature Communications

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Rapid progression through the cell cycle ensures efficient migration of primordial germ cells – The role of Hsp90

(2018) Jana Pfeiffer et al.   DEVELOPMENTAL BIOLOGY

Noncanonical translation via deadenylated 3′ UTRs maintains primordial germ cells

(2018) Youngnam N. Jin et al.   Nature Chemical Biology

Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte

(2018) Peter W. S. Hill et al.   NATURE

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(2018) Ksenia Skvortsova et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development

(2018) Xuefei Yuan et al.   Nature Communications

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

(2017) Laia Ribas et al.   Epigenetics & Chromatin

DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells

(2016) Hongshan Guo et al.   CELL RESEARCH

Chromatin Control of Developmental Dynamics and Plasticity

(2016) Matteo Perino et al.   DEVELOPMENTAL CELL

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(2016) Tommaso Pozzobon et al.   IMMUNOLOGY LETTERS

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

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(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Repulsive cues combined with physical barriers and cell–cell adhesion determine progenitor cell positioning during organogenesis

(2016) Azadeh Paksa et al.   Nature Communications

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

DNA Demethylation Dynamics in the Human Prenatal Germline

(2015) Sofia Gkountela et al.   CELL

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

Chemokine-Dependent pH Elevation at the Cell Front Sustains Polarity in Directionally Migrating Zebrafish Germ Cells

(2015) Katsiaryna Tarbashevich et al.   CURRENT BIOLOGY

Zebrafish germ cells: motility and guided migration

(2015) Azadeh Paksa et al.   CURRENT OPINION IN CELL BIOLOGY

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(2015) Anne J Ridley   CURRENT OPINION IN CELL BIOLOGY

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

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(2015) M. Uhlen et al.   SCIENCE

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence

(2015) Cheng Li et al.   Cell Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Differential Genes Expression between Fertile and Infertile Spermatozoa Revealed by Transcriptome Analysis

(2015) Sandeep Kumar Bansal et al.   PLoS One

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

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

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Chromatin and Transcription Transitions of Mammalian Adult Germline Stem Cells and Spermatogenesis

(2014) Saher Sue Hammoud et al.   Cell Stem Cell

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

Regulatory Principles of Pluripotency: From the Ground State Up

(2014) Jamie A. Hackett et al.   Cell Stem Cell

Antagonistic roles of ubiquitin ligase HEI10 and SUMO ligase RNF212 regulate meiotic recombination

(2014) Huanyu Qiao et al.   NATURE GENETICS

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits

(2013) Yuanchao Xue et al.   CELL

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos

(2013) Lan Jiang et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

Plasticity in Dnmt3L-dependent and -independent modes of de novo methylation in the developing mouse embryo

(2013) M. Guenatri et al.   DEVELOPMENT

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

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(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

GPAT2, a mitochondrial outer membrane protein, in piRNA biogenesis in germline stem cells

(2013) Y. Shiromoto et al.   RNA

Cell–cell adhesion genes CTNNA2 and CTNNA3 are tumour suppressors frequently mutated in laryngeal carcinomas

(2013) Miriam Fanjul-Fernández et al.   Nature Communications

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

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(2012) Alexander Dobin et al.   BIOINFORMATICS

nanos3 maintains germline stem cells and expression of the conserved germline stem cell gene nanos2 in the zebrafish ovary

(2012) Rebecca L. Beer et al.   DEVELOPMENTAL BIOLOGY

5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development

(2012) Rimple D. Almeida et al.   Epigenetics

Global profiling of DNA methylation erasure in mouse primordial germ cells

(2012) S. Guibert et al.   GENOME RESEARCH

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

New insights into establishment and maintenance of DNA methylation imprints in mammals

(2012) G. Kelsey et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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(2012) Hunter B Fraser et al.   GENOME BIOLOGY

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Regulation of hub mRNA stability and translation by miR430 and the dead end protein promotes preferential expression in zebrafish primordial germ cells

(2011) Michaela Mickoleit et al.   DEVELOPMENTAL DYNAMICS

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

(2011) Ozren Bogdanović et al.   GENOME RESEARCH

The biology of cancer testis antigens: Putative function, regulation and therapeutic potential

(2011) Elisabetta Fratta et al.   Molecular Oncology

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

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

(2011) Mark Wossidlo et al.   Nature Communications

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Structure and Function of Mammalian DNA Methyltransferases

(2010) Renata Zofia Jurkowska et al.   CHEMBIOCHEM

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

(2010) Christian Popp et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A Signaling Principle for the Specification of the Germ Cell Lineage in Mice

(2009) Yasuhide Ohinata et al.   CELL

Mechanisms guiding primordial germ cell migration: strategies from different organisms

(2009) Brian E. Richardson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Control over the morphology and segregation of Zebrafish germ cell granules during embryonic development

(2008) Markus J Strasser et al.   BMC DEVELOPMENTAL BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH

Sequence Variants in the RNF212 Gene Associate with Genome-Wide Recombination Rate

(2008) A. Kong et al.   SCIENCE

CpG island density and its correlations with genomic features in mammalian genomes

(2008) Leng Han et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY