Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Widespread Enhancer Dememorization and Promoter Priming during Parental-to-Zygotic Transition

(2018) Bingjie Zhang et al.   MOLECULAR CELL

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

(2017) Fides Zenk et al.   SCIENCE

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

(2017) Shai R Joseph et al.   eLife

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

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

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

(2016) Bluma J Lesch et al.   NATURE GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

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

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

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

(2013) Miler T. Lee et al.   NATURE

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

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Asymmetric Division of Drosophila Male Germline Stem Cell Shows Asymmetric Histone Distribution

(2012) V. Tran et al.   SCIENCE

The zebrafish transcriptome during early development

(2011) Liselotte Vesterlund et al.   BMC DEVELOPMENTAL BIOLOGY

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

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

Partitioning of Histone H3-H4 Tetramers During DNA Replication-Dependent Chromatin Assembly

(2010) M. Xu et al.   SCIENCE

Dissection of Organs from the Adult Zebrafish

(2010) Tripti Gupta et al.   Jove-Journal of Visualized Experiments

Distinctive chromatin in human sperm packages genes for embryo development

(2009) Saher Sue Hammoud et al.   NATURE

Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment

(2008) Amy T McCurley et al.   BMC MOLECULAR BIOLOGY

A rapid micro chromatin immunoprecipitation assay (ChIP)

(2008) John Arne Dahl 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

Multigene Phylogeny of Choanozoa and the Origin of Animals

(2008) Kamran Shalchian-Tabrizi et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY