Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

(2017) Fides Zenk et al.   SCIENCE

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

(2017) Yimeng Yin et al.   SCIENCE

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Sperm is epigenetically programmed to regulate gene transcription in embryos

(2016) Marta Teperek et al.   GENOME RESEARCH

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

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

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

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

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(2015) K. Siklenka et al.   SCIENCE

Reprogramming the genome to totipotency in mouse embryos

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

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

(2015) Hyung Joo Lee et al.   Nature Communications

Uniformity of Nucleosome Preservation Pattern in Mammalian Sperm and Its Connection to Repetitive DNA Elements

(2014) Birgit Samans et al.   DEVELOPMENTAL CELL

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

(2014) Benjamin R. Carone et al.   DEVELOPMENTAL CELL

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

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

The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species

(2014) Patricia Heyn et al.   Cell Reports

Paternal Poly (ADP-ribose) Metabolism Modulates Retention of Inheritable Sperm Histones and Early Embryonic Gene Expression

(2014) Motomasa Ihara et al.   PLoS Genetics

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

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

(2013) Miler T. Lee et al.   NATURE

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

(2013) Yael Costa et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

DNA methylation: roles in mammalian development

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

Spatial expression of transcription factors in Drosophila embryonic organ development

(2013) Ann S Hammonds et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Developmental features of DNA methylation during activation of the embryonic zebrafish genome

(2012) Ingrid S Andersen et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation

(2011) Leif C. Lindeman et al.   DEVELOPMENTAL CELL

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

(2011) S.-F. Wu et al.   GENOME RESEARCH

CpG Islands Recruit a Histone H3 Lysine 36 Demethylase

(2010) Neil P. Blackledge et al.   MOLECULAR CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

(2010) Urszula Brykczynska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chd1 regulates open chromatin and pluripotency of embryonic stem cells

(2009) Alexandre Gaspar-Maia et al.   NATURE

Distinctive chromatin in human sperm packages genes for embryo development

(2009) Saher Sue Hammoud et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY