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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1107s32openalex-snapshot

Aligning Short Sequencing Reads with Bowtie

inferredcites →https://doi.org/10.1002/j.1460-2075.1995.tb07255.xopenalex-snapshot

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

inferredcites →https://doi.org/10.1016/j.cub.2014.04.032openalex-snapshot

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

inferredcites →https://doi.org/10.1016/j.gde.2004.07.004openalex-snapshot

Whole-genome analysis of Drosophila gastrulation

inferredcites →https://doi.org/10.1016/j.gde.2015.12.003openalex-snapshot

Pioneer transcription factors, chromatin dynamics, and cell fate control

inferredcites →https://doi.org/10.1016/j.molcel.2008.02.010openalex-snapshot

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

inferredcites →https://doi.org/10.1016/j.molcel.2012.10.019openalex-snapshot

Nucleosome-Driven Transcription Factor Binding and Gene Regulation

inferredcites →https://doi.org/10.1016/j.molcel.2014.04.006openalex-snapshot

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

inferredcites →https://doi.org/10.1016/s0092-8674(02)01087-5openalex-snapshot

Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo

inferredcites →https://doi.org/10.1016/s0092-8674(04)00044-3openalex-snapshot

The Nucleosome

inferredcites →https://doi.org/10.1016/s0959-437x(99)80022-7openalex-snapshot

Chromatin-modifying and -remodeling complexes

inferredcites →https://doi.org/10.1038/324537a0openalex-snapshot

A molecular gradient in early Drosophila embryos and its role in specifying the body pattern

inferredcites →https://doi.org/10.1038/nature07388openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature09990openalex-snapshot

A cis-regulatory map of the Drosophila genome

inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot

The accessible chromatin landscape of the human genome

inferredcites →https://doi.org/10.1038/nature13395openalex-snapshot

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

inferredcites →https://doi.org/10.1038/nbt.2798openalex-snapshot

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

inferredcites →https://doi.org/10.1038/ng.2305openalex-snapshot

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

inferredcites →https://doi.org/10.1038/ng.808openalex-snapshot

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot

Transcription factors: from enhancer binding to developmental control

inferredcites →https://doi.org/10.1073/pnas.0407387101openalex-snapshot

Discovery of functional noncoding elements by digital analysis of chromatin structure

inferredcites →https://doi.org/10.1073/pnas.0912395106openalex-snapshot

Dynamics of the Dorsal morphogen gradient

inferredcites →https://doi.org/10.1073/pnas.0913805107openalex-snapshot

Nucleosome-mediated cooperativity between transcription factors

inferredcites →https://doi.org/10.1093/bioinformatics/15.7.563openalex-snapshot

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.

inferredcites →https://doi.org/10.1093/nar/gkv978openalex-snapshot

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster

inferredcites →https://doi.org/10.1101/gad.10.13.1670openalex-snapshot

Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control.

inferredcites →https://doi.org/10.1101/gad.1509007openalex-snapshot

A core transcriptional network for early mesoderm development in Drosophila melanogaster

inferredcites →https://doi.org/10.1101/gad.176826.111openalex-snapshot

Pioneer transcription factors: establishing competence for gene expression

inferredcites →https://doi.org/10.1101/gad.1861209openalex-snapshot

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

inferredcites →https://doi.org/10.1101/gad.234534.113openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.5.9.1568openalex-snapshot

twist and snail as positive and negative regulators during Drosophila mesoderm development.

inferredcites →https://doi.org/10.1101/gr.121541.111openalex-snapshot

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

inferredcites →https://doi.org/10.1101/gr.151472.112openalex-snapshot

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

inferredcites →https://doi.org/10.1101/gr.192542.115openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.5655606openalex-snapshot

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection

inferredcites →https://doi.org/10.1126/science.1065175openalex-snapshot

Regulation of Organogenesis by the Caenorhabditis elegans FoxA Protein PHA-4

inferredcites →https://doi.org/10.1126/science.1160631openalex-snapshot

Shadow Enhancers as a Source of Evolutionary Novelty

inferredcites →https://doi.org/10.1128/mcb.23.5.1623-1632.2003openalex-snapshot

Collaborative Competition Mechanism for Gene Activation In Vivo

inferredcites →https://doi.org/10.1146/annurev-genet-110711-155437openalex-snapshot

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

inferredcites →https://doi.org/10.1186/gb-2007-8-7-r145openalex-snapshot

Global analysis of patterns of gene expression during Drosophilaembryogenesis

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/gb-2009-10-7-r80openalex-snapshot

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

inferredcites →https://doi.org/10.1186/gb-2011-12-4-r34openalex-snapshot

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

inferredcites →https://doi.org/10.1186/gb-2013-14-12-r140openalex-snapshot

Spatial expression of transcription factors in Drosophilaembryonic organ development

inferredcites →https://doi.org/10.1242/dev.01124openalex-snapshot

A regulatory code for neurogenic gene expression in theDrosophilaembryo

inferredcites →https://doi.org/10.1242/dev.02373openalex-snapshot

The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription

inferredcites →https://doi.org/10.1242/dev.121.9.3067openalex-snapshot

Posterior stripe expression of hunchback is driven from two promoters by a common enhancer element

inferredcites →https://doi.org/10.1242/dev.133900openalex-snapshot

Cell fate control by pioneer transcription factors

inferredcites →https://doi.org/10.1371/journal.pbio.0060027openalex-snapshot

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

inferredcites →https://doi.org/10.1371/journal.pbio.0060263openalex-snapshot

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

inferredcites →https://doi.org/10.1371/journal.pbio.1000343openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pbio.1000590openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1002266openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1002339openalex-snapshot

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

inferredcites →https://doi.org/10.1371/journal.pone.0009129openalex-snapshot

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

inferredcites →https://doi.org/10.1534/genetics.116.186783openalex-snapshot

Quantitative Single-Embryo Profile ofDrosophilaGenome Activation and the Dorsal–Ventral Patterning Network

inferredcites →https://doi.org/10.17615/nvtt-9k83openalex-snapshot

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

inferredcites →https://doi.org/10.7554/elife.03737openalex-snapshot

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

inferredcites →https://doi.org/10.7554/elife.20148openalex-snapshot

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

inferredcites →https://doi.org/10.7554/elife.28275openalex-snapshot

Concentration dependent chromatin states induced by the bicoid morphogen gradient

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cub.2019.03.019openalex-snapshot

The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

inferred← citeshttps://doi.org/10.1016/j.devcel.2023.07.007openalex-snapshot

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

inferred← citeshttps://doi.org/10.1101/2020.10.21.348722openalex-snapshot

Context dependent activation and repression of enhancers by Hunchback binding sites in Drosophila embryo

inferred← citeshttps://doi.org/10.1101/2021.07.10.451524openalex-snapshot

Minimal Synthetic Enhancers Reveal Control of the Probability of Transcriptional Engagement and its Timing by a Morphogen Gradient

inferred← citeshttps://doi.org/10.1146/annurev-cellbio-020823-011522openalex-snapshot

Control of Tissue Development by Morphogens

inferred← citeshttps://doi.org/10.1242/dev.196113openalex-snapshot

Dynamic patterning by morphogens illuminated by cis-regulatory studies

inferred← citeshttps://doi.org/10.64898/2026.02.23.707495openalex-snapshot

The Zelda Interactome Reveals Diverse Co-factors Essential for Pioneer Factor-Mediated Zygotic Genome Activation

inferred← citeshttps://doi.org/10.7554/elife.56429openalex-snapshot

Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility

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