Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster

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

(2018) Lei Gao et al.   CELL

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

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome

(2018) Emily G. Kaye et al.   Cell Reports

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

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

Rif1 prolongs the embryonic S phase at the Drosophila mid-blastula transition

(2018) Charles A. Seller et al.   PLOS BIOLOGY

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

Chromatin remodeling in Drosophila preblastodermic embryo extract

(2018) Eva Šatović et al.   Scientific Reports

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP

(2017) Leila E. Rieder et al.   GENES & DEVELOPMENT

Ploidy has little effect on timing early embryonic events in the haplo-diploid wasp Nasonia

(2017) Deanna Arsala et al.   GENESIS

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

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

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

A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster

(2017) Danielle C. Hamm et al.   PLoS Genetics

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

(2017) Lupis Ribeiro et al.   PLoS Genetics

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

(2017) Shai R Joseph et al.   eLife

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

Concentration dependent chromatin states induced by the bicoid morphogen gradient

(2017) Colleen E Hannon et al.   eLife

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

(2017) Yun Huang et al.   eLife

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

(2017) Michael R Stadler et al.   eLife

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Oocyte-expressed yes-associated protein is a key activator of the early zygotic genome in mouse

(2016) Chao Yu et al.   CELL RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

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

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

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

(2016) Kai Yuan et al.   TRENDS IN GENETICS

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos

(2016) Stephen W Eichhorn et al.   eLife

Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition

(2015) Shelby A. Blythe et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle

(2015) S. P. Hergeth et al.   EMBO REPORTS

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

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

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

Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

(2015) Bridlin Barckmann et al.   Cell Reports

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

(2015) Nicholas J. Fuda et al.   PLoS Genetics

Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

(2015) John D Laver et al.   GENOME BIOLOGY

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

(2014) Peng Yang et al.   BIOESSAYS

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Co-activation of microRNAs by Zelda is essential for early Drosophila development

(2014) S. Fu et al.   DEVELOPMENT

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila

(2014) Z. Xu et al.   GENES & DEVELOPMENT

Pioneer transcription factors in cell reprogramming

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

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

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila

(2014) Carlo G. Artieri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

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

(2014) Patricia Heyn et al.   Cell Reports

Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development

(2014) Leonardo Gastón Guilgur et al.   eLife

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

(2014) Xiao-Yong Li et al.   eLife

3D imaging of Sox2 enhancer clusters in embryonic stem cells

(2014) Zhe Liu et al.   eLife

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein

(2014) Linan Chen et al.   GENOME BIOLOGY

Deadenylation of mRNA by the CCR4–NOT complex in Drosophila: molecular and developmental aspects

(2014) Claudia Temme et al.   Frontiers in Genetics

Chromatin dynamics during spermiogenesis

(2013) Christina Rathke et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha 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

Posttranslational Control of Cdc25 Degradation Terminates Drosophila’s Early Cell-Cycle Program

(2013) Stefano Di Talia 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

Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila

(2013) Jun Cui et al.   DEVELOPMENTAL BIOLOGY

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

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

The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation

(2013) M. M. L. Soruco et al.   GENES & DEVELOPMENT

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

(2013) Miler T. Lee et al.   NATURE

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

The CCR4 Deadenylase Acts with Nanos and Pumilio in the Fine-Tuning of Mei-P26 Expression to Promote Germline Stem Cell Self-Renewal

(2013) Willy Joly et al.   Stem Cell Reports

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Embryonic onset of late replication requires Cdc25 down-regulation

(2012) J. A. Farrell et al.   GENES & DEVELOPMENT

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

RNA Targets and Specificity of Staufen, a Double-stranded RNA-binding Protein inCaenorhabditis elegans

(2012) Jacqueline Baca LeGendre et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Identification of Early Zygotic Genes in the Yellow Fever Mosquito Aedes aegypti and Discovery of a Motif Involved in Early Zygotic Genome Activation

(2012) James K. Biedler et al.   PLoS One

Replacement of H1 linker histone during bovine somatic cell nuclear transfer

(2012) Yan Yun et al.   THERIOGENOLOGY

Histone H1 Depletion Impairs Embryonic Stem Cell Differentiation

(2012) Yunzhe Zhang et al.   PLoS Genetics

Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo

(2011) A. Burton et al.   Briefings in Functional Genomics

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

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

Pioneer transcription factors: establishing competence for gene expression

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

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

(2011) Susan E. Lott et al.   PLOS BIOLOGY

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

(2011) Amy Tsurumi et al.   PLoS 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

Developmental Control of Late Replication and S Phase Length

(2010) Antony W. Shermoen et al.   CURRENT BIOLOGY

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

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

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo

(2010) Christel Rouget et al.   NATURE

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

(2010) C. Temme et al.   RNA

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Genome-wide analysis of mRNA decay patterns during early Drosophila development

(2010) Stefan Thomsen et al.   GENOME BIOLOGY

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

Dynamic alterations of linker histone variants during development

(2009) James S. Godde et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

DNA replication times the cell cycle and contributes to the mid-blastula transition inDrosophilaembryos

(2009) Mark L. McCleland et al.   JOURNAL OF CELL BIOLOGY

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

(2009) Barrett C Foat et al.   Molecular Systems Biology

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

(2009) E. Lund et al.   RNA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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

(2008) Natascha Bushati et al.   CURRENT BIOLOGY

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

(2008) Hsiao-Lan Liang et al.   NATURE