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

https://doi.org/10.1371/journal.pgen.1002266

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What this work says

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Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation

inferred← citeshttps://doi.org/10.1038/s41586-022-04680-7openalex-snapshot

Transcriptional coupling of distant regulatory genes in living embryos

inferred← citeshttps://doi.org/10.1038/s41588-021-00799-xopenalex-snapshot

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

inferred← citeshttps://doi.org/10.1038/s41588-021-00816-zopenalex-snapshot

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

inferred← citeshttps://doi.org/10.1038/s41588-026-02503-3openalex-snapshot

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila

inferred← citeshttps://doi.org/10.1038/s41594-024-01231-8openalex-snapshot

Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function

inferred← citeshttps://doi.org/10.1038/s41598-026-35953-0openalex-snapshot

The functional organization of chromosome territories in single nuclei during zygotic genome activation

inferred← citeshttps://doi.org/10.1038/s43586-020-00008-9openalex-snapshot

Chromatin accessibility profiling methods

inferred← citeshttps://doi.org/10.1038/s44319-024-00245-zopenalex-snapshot

Epigenetic inheritance and gene expression regulation in early Drosophila embryos

inferred← citeshttps://doi.org/10.1038/s44319-025-00397-6openalex-snapshot

Muskelin is a substrate adaptor of the highly regulated Drosophila embryonic CTLH E3 ligase

inferred← citeshttps://doi.org/10.1038/s44319-025-00596-1openalex-snapshot

Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation

inferred← citeshttps://doi.org/10.1038/s44320-024-00014-zopenalex-snapshot

Canalizing cell fate by transcriptional repression

inferred← citeshttps://doi.org/10.1042/bst20200873openalex-snapshot

Keeping your options open: insights from Dppa2/4 into how epigenetic priming factors promote cell plasticity

inferred← citeshttps://doi.org/10.1063/1.4808157openalex-snapshot

Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in theDrosophilaembryo

inferred← citeshttps://doi.org/10.1073/pnas.1317034110openalex-snapshot

Taf7l cooperates with Trf2 to regulate spermiogenesis

inferred← citeshttps://doi.org/10.1073/pnas.1516450113openalex-snapshot

Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan

inferred← citeshttps://doi.org/10.1073/pnas.1703001114openalex-snapshot

Broadly expressed repressors integrate patterning across orthogonal axes in embryos

inferred← citeshttps://doi.org/10.1073/pnas.1711236115openalex-snapshot

Iterative random forests to discover predictive and stable high-order interactions

inferred← citeshttps://doi.org/10.1073/pnas.2531899123openalex-snapshot

Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation

inferred← citeshttps://doi.org/10.1074/jbc.m114.602292openalex-snapshot

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

inferred← citeshttps://doi.org/10.1080/19336934.2016.1188231openalex-snapshot

Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control

inferred← citeshttps://doi.org/10.1083/jcb.201710038openalex-snapshot

Visualizing transcription factor dynamics in living cells

inferred← citeshttps://doi.org/10.1083/jcb.201807044openalex-snapshot

Genomic insights into chromatin reprogramming to totipotency in embryos

inferred← citeshttps://doi.org/10.1083/jcb.202412222openalex-snapshot

Spatially ordered zygotic genome activation fulfills embryo quality control

inferred← citeshttps://doi.org/10.1091/mbc.e24-01-0028openalex-snapshot

Zelda is dispensable for Drosophila melanogaster histone gene regulation

inferred← citeshttps://doi.org/10.1093/bfgp/els034openalex-snapshot

Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1093/g3journal/jkac159openalex-snapshot

Premature translation of the Drosophila zygotic genome activator Zelda is not sufficient to precociously activate gene expression

inferred← citeshttps://doi.org/10.1093/g3journal/jkag159openalex-snapshot

Enhancer RNA transcription near segmentation gene enhancers can be analyzed in situ using FISH

inferred← citeshttps://doi.org/10.1093/gbe/evt077openalex-snapshot

Fungal Genes in Context: Genome Architecture Reflects Regulatory Complexity and Function

inferred← citeshttps://doi.org/10.1093/gbe/evv080openalex-snapshot

What Does It Take to Evolve an Enhancer? A Simulation-Based Study of Factors Influencing the Emergence of Combinatorial Regulation

inferred← citeshttps://doi.org/10.1093/gbe/evz103openalex-snapshot

The Role of Chromatin Accessibility in cis-Regulatory Evolution

inferred← citeshttps://doi.org/10.1093/genetics/iyab107openalex-snapshot

CLAMP regulates zygotic genome activation in Drosophila embryos

inferred← citeshttps://doi.org/10.1093/genetics/iyac111openalex-snapshot

Transcription factors perform a 2-step search of the nucleus

inferred← citeshttps://doi.org/10.1093/genetics/iyad142openalex-snapshot

Setting the stage for development: the maternal-to-zygotic transition in Drosophila

inferred← citeshttps://doi.org/10.1093/molbev/mst170openalex-snapshot

Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

inferred← citeshttps://doi.org/10.1093/nar/gkab1177openalex-snapshot

Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos

inferred← citeshttps://doi.org/10.1093/nar/gkaf516openalex-snapshot

Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome

inferred← citeshttps://doi.org/10.1093/nar/gks543openalex-snapshot

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

inferred← citeshttps://doi.org/10.1093/nar/gkt1302openalex-snapshot

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

inferred← citeshttps://doi.org/10.1093/nar/gkt598openalex-snapshot

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

inferred← citeshttps://doi.org/10.1093/nar/gkt702openalex-snapshot

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

inferred← citeshttps://doi.org/10.1093/nar/gkt831openalex-snapshot

A general approach for discriminative de novo motif discovery from high-throughput data

inferred← citeshttps://doi.org/10.1093/nar/gkv195openalex-snapshot

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

inferred← citeshttps://doi.org/10.1098/rsob.180183openalex-snapshot

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

inferred← citeshttps://doi.org/10.1101/129577openalex-snapshot

A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

inferred← citeshttps://doi.org/10.1101/2020.02.03.931972openalex-snapshot

Continual inactivation of genes involved in stem cell functional identity stabilizes progenitor commitment

inferred← citeshttps://doi.org/10.1101/2020.07.15.204248openalex-snapshot

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

inferred← citeshttps://doi.org/10.1101/2020.07.15.205054openalex-snapshot

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

inferred← citeshttps://doi.org/10.1101/2020.09.01.278796openalex-snapshot

Synergistic activity of Nanog, Pou5f3, and Sox19b establishes chromatin accessibility and developmental competence in a context-dependent manner

inferred← citeshttps://doi.org/10.1101/2021.01.08.425929openalex-snapshot

An “individualist” model of an active genome in a developing embryo

inferred← citeshttps://doi.org/10.1101/2021.02.25.432925openalex-snapshot

Defining kinetic roles of transcriptional activators in the early Drosophila embryo

inferred← citeshttps://doi.org/10.1101/2021.03.18.435761openalex-snapshot

Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryo

inferred← citeshttps://doi.org/10.1101/2022.03.22.485419openalex-snapshot

Premature translation of the zygotic genome activator Zelda is not sufficient to precociously activate gene expression

inferred← citeshttps://doi.org/10.1101/2022.06.02.494376openalex-snapshot

Enhancer architecture and chromatin accessibility constrain phenotypic space during development

inferred← citeshttps://doi.org/10.1101/2022.12.12.520036openalex-snapshot

3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

inferred← citeshttps://doi.org/10.1101/2022.12.15.519123openalex-snapshot

Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos

inferred← citeshttps://doi.org/10.1101/2023.11.01.565184openalex-snapshot

OVO Positively Regulates Essential Maternal Pathways by Binding Near the Transcriptional Start Sites in the Drosophila Female Germline

inferred← citeshttps://doi.org/10.1101/2024.04.16.589811openalex-snapshot

A fine kinetic balance of interactions directs transcription factor hubs to genes

inferred← citeshttps://doi.org/10.1101/2024.06.28.601265openalex-snapshot

Muskelin acts as a substrate receptor of the highly regulated Drosophila CTLH E3 ligase during the maternal-to-zygotic transition

inferred← citeshttps://doi.org/10.1101/2024.08.14.607943openalex-snapshot

Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome

inferred← citeshttps://doi.org/10.1101/2025.01.08.631745openalex-snapshot

Single-nucleus multiome ATAC and RNA sequencing reveals the molecular basis of thermal acclimation in Drosophila melanogaster embryos

inferred← citeshttps://doi.org/10.1101/2025.01.13.632851openalex-snapshot

Breaking anterior-posterior symmetry in the moth fly Clogmia albipunctata

inferred← citeshttps://doi.org/10.1101/2025.02.11.636561openalex-snapshot

Balancing precision with plasticity: Redefining the roles of transcription factors in early cell fate specification

inferred← citeshttps://doi.org/10.1101/2025.10.06.680768openalex-snapshot

Differential usage of two, distinct DNA-binding domains regulates tissue-specific occupancy of the pioneer factor Zelda

inferred← citeshttps://doi.org/10.1101/324582openalex-snapshot

The Sheep and the Goats: Distinguishing transcriptional enhancers in a complex chromatin landscape

inferred← citeshttps://doi.org/10.1101/369231openalex-snapshot

Brd4 and P300 regulate zygotic genome activation through histone acetylation

inferred← citeshttps://doi.org/10.1101/379974openalex-snapshot

Mutation of sequences flanking and separating transcription factor binding sites in a Drosophila enhancer significantly alter its output

inferred← citeshttps://doi.org/10.1101/380857openalex-snapshot

Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during early Drosophila melanogaster embryogenesis

inferred← citeshttps://doi.org/10.1101/385070openalex-snapshot

Effects of the maternal factor Zelda on zygotic enhancer activity in the Drosophila embryo

inferred← citeshttps://doi.org/10.1101/516500openalex-snapshot

Genome-wide Prediction of Potential Polycomb Response Elements and their Functions

inferred← citeshttps://doi.org/10.1101/720102openalex-snapshot

TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish

inferred← citeshttps://doi.org/10.1101/gad.188052.112openalex-snapshot

HOT regions function as patterned developmental enhancers and have a distinct cis -regulatory signature

inferred← citeshttps://doi.org/10.1101/gad.192583.112openalex-snapshot

HOT DNAs: a novel class of developmental enhancers: Figure 1.

inferred← citeshttps://doi.org/10.1101/gad.215137.113openalex-snapshot

Transcriptional elongation checkpoint control in development and disease

inferred← citeshttps://doi.org/10.1101/gad.215459.113openalex-snapshot

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

inferred← citeshttps://doi.org/10.1101/gad.230953.113openalex-snapshot

A conserved role for Snail as a potentiator of active transcription

inferred← citeshttps://doi.org/10.1101/gad.234534.113openalex-snapshot

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

inferred← citeshttps://doi.org/10.1101/gad.253443.114openalex-snapshot

Pioneer transcription factors in cell reprogramming

inferred← citeshttps://doi.org/10.1101/gad.305078.117openalex-snapshot

Dense Bicoid hubs accentuate binding along the morphogen gradient

inferred← citeshttps://doi.org/10.1101/gad.352572.124openalex-snapshot

Sex-specific transcriptome dynamics of Anopheles gambiae during embryonic development

inferred← citeshttps://doi.org/10.1101/gr.132811.111openalex-snapshot

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

inferred← citeshttps://doi.org/10.1101/gr.192542.115openalex-snapshot

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

inferred← citeshttps://doi.org/10.1101/gr.209486.116openalex-snapshot

Drosophila poised enhancers are generated during tissue patterning with the help of repression

inferred← citeshttps://doi.org/10.1101/gr.242164.118openalex-snapshot

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

inferred← citeshttps://doi.org/10.1111/febs.14856openalex-snapshot

Zelda and the maternal‐to‐zygotic transition in cockroaches

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