The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation

Pioneering the developmental frontier

(2021) Elizabeth D. Larson et al.   MOLECULAR CELL

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

(2020) Máté Pálfy et al.   PLoS Genetics

Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones

(2020) Makiko Iwafuchi et al.   NATURE GENETICS

LabxDB: Versatile databases for genomic sequencing and lab management

(2020) Charles E Vejnar et al.   BIOINFORMATICS

Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation

(2020) Maria Samata et al.   CELL

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

(2019) Huaiyu Mi et al.   Nature Protocols

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

(2019) Marina Veil et al.   GENOME RESEARCH

The maternal-to-zygotic transition revisited

(2019) Nadine L. Vastenhouw et al.   DEVELOPMENT

Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation

(2019) Shun Hang Chan et al.   DEVELOPMENTAL CELL

Resetting histone modifications during human parental-to-zygotic transition

(2019) Weikun Xia et al.   SCIENCE

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis

(2019) Yuko Sato et al.   DEVELOPMENT

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

Combinatorial action of NF–Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish

(2019) William Stanney et al.   DEVELOPMENTAL BIOLOGY

Mediator complex component MED13 regulates zygotic genome activation and is required for postimplantation development in the mouse†,‡

(2018) Yi-Liang Miao et al.   BIOLOGY OF REPRODUCTION

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

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

(2018) Guifen Liu et al.   GENOME RESEARCH

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

The mechanistic basis for chromatin regulation by pioneer transcription factors

(2018) Makiko Iwafuchi-Doi   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Genomic insights into chromatin reprogramming to totipotency in embryos

(2018) Sabrina Ladstätter et al.   JOURNAL OF CELL BIOLOGY

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

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

(2018) Bingjie Zhang et al.   MOLECULAR CELL

Mechanisms regulating zygotic genome activation

(2018) Katharine N. Schulz et al.   NATURE REVIEWS GENETICS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

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

(2017) M Ryan Corces et al.   NATURE METHODS

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

(2017) Shai R Joseph et al.   eLife

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

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

The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

(2016) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

(2014) Andrew C Nelson et al.   BMC BIOLOGY

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Discovery and Optimization of Small-Molecule Ligands for the CBP/p300 Bromodomains

(2014) Duncan A. Hay et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

Coactivators p300 and CBP Maintain the Identity of Mouse Embryonic Stem Cells by Mediating Long-Range Chromatin Structure

(2014) Fang Fang et al.   STEM CELLS

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

(2014) Patricia Heyn et al.   Cell Reports

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

(2014) Xiao-Yong Li et al.   eLife

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

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos

(2013) Ozren Bogdanović et al.   METHODS

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

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

(2013) Miler T. Lee 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

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway

(2012) Cong Xu et al.   DEVELOPMENTAL CELL

Nucleosome-Driven Transcription Factor Binding and Gene Regulation

(2012) Cecilia Ballaré et al.   MOLECULAR CELL

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

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Dynamics of Nucleosome Invasion by DNA Binding Proteins

(2011) Hannah S. Tims et al.   JOURNAL OF MOLECULAR BIOLOGY

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming

(2010) Antonio J Giraldez   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

(2010) Rachel E. Haurwitz et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Small ubiquitin-related modifier paralogs are indispensable but functionally redundant during early development of zebrafish

(2009) Hao Yuan et al.   CELL RESEARCH

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

(2009) W. Tadros et al.   DEVELOPMENT

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Brd4 associates with mitotic chromosomes throughout early zebrafish embryogenesis

(2008) Reiko Toyama et al.   DEVELOPMENTAL DYNAMICS

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY