Mechanisms regulating zygotic genome activation

LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos

(2018) Jacques P. Bothma et al.   CELL

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

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders 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

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

(2018) Qianhua Xu et al.   TRENDS IN CELL BIOLOGY

Sperm nuclear protamines: A checkpoint to control sperm chromatin quality

(2018) Klaus Steger et al.   ANATOMIA HISTOLOGIA EMBRYOLOGIA

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

High-throughput chromatin accessibility profiling at single-cell resolution

(2018) Anja Mezger et al.   Nature Communications

The Birth of the 3D Genome during Early Embryonic Development

(2018) Clemens B. Hug et al.   TRENDS IN GENETICS

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence

(2017) Ivayla Ivanova et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition

(2017) Boxuan Simen Zhao et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Genome editing reveals a role for OCT4 in human embryogenesis

(2017) Norah M. E. Fogarty et al.   NATURE

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

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

Conservation and innovation in the DUX4-family gene network

(2017) Jennifer L Whiddon et al.   NATURE GENETICS

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

Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects

(2017) Lupis Ribeiro et al.   PLoS Genetics

Both Nuclear Size and DNA Amount Contribute to Midblastula Transition Timing in Xenopus laevis

(2017) Predrag Jevtić et al.   Scientific Reports

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Transcriptional Memory in the Drosophila Embryo

(2016) Teresa Ferraro et al.   CURRENT BIOLOGY

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

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

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

A decade of transcription factor-mediated reprogramming to pluripotency

(2016) Kazutoshi Takahashi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes

(2016) Si Ho Choi et al.   NUCLEIC ACIDS RESEARCH

Timing the Drosophila Mid-Blastula Transition: A Cell Cycle-Centered View

(2016) Kai Yuan et al.   TRENDS IN GENETICS

Linking Pluripotency Reprogramming and Cancer

(2016) Juan Manuel Iglesias et al.   Stem Cells Translational Medicine

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

Nuclear Size Scaling during Xenopus Early Development Contributes to Midblastula Transition Timing

(2015) Predrag Jevtić et al.   CURRENT BIOLOGY

Dynamic visualization of transcription and RNA subcellular localization in zebrafish

(2015) P. D. Campbell et al.   DEVELOPMENT

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA

(2015) Anupam A. Sawant et al.   NUCLEIC ACIDS RESEARCH

Histone titration against the genome sets the DNA-to-cytoplasm threshold for theXenopusmidblastula transition

(2015) Amanda A. Amodeo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

(2015) Wulan Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogramming the genome to totipotency in mouse embryos

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

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of zygotic genome activation and DNA damage checkpoint acquisition at the mid-blastula transition

(2015) Maomao Zhang et al.   CELL CYCLE

Maternal histone variants and their chaperones promote paternal genome activation and boost somatic cell reprogramming

(2014) Peng Yang et al.   BIOESSAYS

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

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

(2014) Li Shen et al.   Cell Stem Cell

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

(2014) Clara Collart et al.   DEVELOPMENT

Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst

(2014) G. C. Le Bin et al.   DEVELOPMENT

Histone variants: dynamic punctuation in transcription

(2014) C. M. Weber et al.   GENES & DEVELOPMENT

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

(2014) D. M. Messerschmidt et al.   GENES & DEVELOPMENT

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

(2014) S. Takayama et al.   GENOME RESEARCH

Transcriptional Activation Is a Conserved Feature of the Early Embryonic Factor Zelda That Requires a Cluster of Four Zinc Fingers for DNA Binding and a Low-complexity Activation Domain

(2014) Danielle C. Hamm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

(2014) Andrew J. Oldfield et al.   MOLECULAR CELL

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K27me and PRC2 transmit a memory of repression across generations and during development

(2014) L. J. Gaydos et al.   SCIENCE

Transgenerational epigenetics in the germline cycle of Caenorhabditis elegans

(2014) William G Kelly   Epigenetics & Chromatin

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

(2014) Patricia Heyn et al.   Cell Reports

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination

(2013) Marco Nardini 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

Number of Nuclear Divisions in the Drosophila Blastoderm Controlled by Onset of Zygotic Transcription

(2013) Hung-wei Sung et al.   CURRENT BIOLOGY

Mechanism and Regulation of Cdc25/Twine Protein Destruction in Embryonic Cell-Cycle Remodeling

(2013) Jeffrey A. Farrell et al.   CURRENT BIOLOGY

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development

(2013) C.-J. Lin et al.   DEVELOPMENT

Identification of the zebrafish maternal and paternal transcriptomes

(2013) Steven A. Harvey et al.   DEVELOPMENT

The Embryonic Linker Histone H1 Variant of Drosophila, dBigH1, Regulates Zygotic Genome Activation

(2013) Salvador Pérez-Montero et al.   DEVELOPMENTAL CELL

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

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

(2013) Miler T. Lee et al.   NATURE

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

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

Titration of Four Replication Factors Is Essential for the Xenopus laevis Midblastula Transition

(2013) C. Collart et al.   SCIENCE

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

DUX4 Binding to Retroelements Creates Promoters That Are Active in FSHD Muscle and Testis

(2013) Janet M. Young et al.   PLoS Genetics

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

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

(2012) Cong Xu et al.   DEVELOPMENTAL CELL

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

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

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

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

DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy

(2011) Linda N. Geng et al.   DEVELOPMENTAL CELL

Pioneer transcription factors: establishing competence for gene expression

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

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

(2011) Ozren Bogdanović et al.   GENOME RESEARCH

The FSHD Atrophic Myotube Phenotype Is Caused by DUX4 Expression

(2011) Céline Vanderplanck et al.   PLoS One

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes

(2010) Melissa M. Harrison et al.   DEVELOPMENTAL BIOLOGY

β-Catenin Primes Organizer Gene Expression by Recruiting a Histone H3 Arginine 8 Methyltransferase, Prmt2

(2010) Shelby A. Blythe et al.   DEVELOPMENTAL CELL

Foxa1 Functions as a Pioneer Transcription Factor at Transposable Elements to ActivateAfpduring Differentiation of Embryonic Stem Cells

(2010) Joseph H. Taube et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy

(2010) R. J. L. F. Lemmers et al.   SCIENCE

B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo

(2010) Yuichi Okuda et al.   PLoS Genetics

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition

(2009) X. Lu et al.   DEVELOPMENT

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

(2009) W. Tadros et al.   DEVELOPMENT

An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition

(2009) B. Benoit et al.   DEVELOPMENT

Histone H3 lysine 4 (H3K4) methylation in development and differentiation

(2009) Joel C. Eissenberg et al.   DEVELOPMENTAL BIOLOGY

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Deadenylation of maternal mRNAs mediated by miR-427 in Xenopus laevis embryos

(2009) E. Lund et al.   RNA

Global Transcriptional Repression in C. elegans Germline Precursors by Regulated Sequestration of TAF-4

(2008) Tugba Guven-Ozkan et al.   CELL

RNAi of Mitotic Cyclins in Drosophila Uncouples the Nuclear and Centrosome Cycle

(2008) Mark L. McCleland et al.   CURRENT BIOLOGY

Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila

(2008) Natascha Bushati et al.   CURRENT BIOLOGY

Intron Delays and Transcriptional Timing during Development

(2008) Ian A. Swinburne et al.   DEVELOPMENTAL CELL

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Genomic Distribution and Function of Histone Variant HTZ-1 during C. elegans Embryogenesis

(2008) Christina M. Whittle et al.   PLoS Genetics

Alterations of the cytoskeleton in all three embryonic lineages contribute to the epiboly defect of Pou5f1/Oct4 deficient MZspg zebrafish embryos

(2007) Martina Lachnit et al.   DEVELOPMENTAL BIOLOGY