ArticlePLoS genetics2013
Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 49 citations in OpenAlex.
- Epigenomics and transcriptomics profiles of developing zebrafish heart cells.Scientific data · 2025Article
- Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.Genome biology · 2025Article
- The Multifaceted Roles of Zinc Finger Proteins in Pluripotency and Reprogramming.International journal of molecular sciences · 2025Review
- Zic3 enables bimodal regulation of tyrosine hydroxylase expression in olfactory bulb and midbrain-derived neurons.Cell death discovery · 2025Article
- Breaking Left-Right Symmetry by the Interplay of Planar Cell Polarity, Calcium Signaling and Cilia.Cells · 2024Review
- Transcriptome and acetylome profiling identify crucial steps of neuronal differentiation in Rubinstein-Taybi syndrome.Communications biology · 2024Article
- Canonical and Non-Canonical Wnt Signaling Generates Molecular and Cellular Asymmetries to Establish Embryonic Axes.Journal of developmental biology · 2024Review
- Dolutegravir and Folic Acid Interaction during Neural System Development in Zebrafish Embryos.International journal of molecular sciences · 2024Article
- Loss of Zic3 impairs planar cell polarity leading to abnormal left-right signaling, heart defects and neural tube defects.Human molecular genetics · 2021Article
- Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region.Cellular and molecular life sciences : CMLS · 2021Article
- RNA polymerase II clusters form in line with surface condensation on regulatory chromatin.Molecular systems biology · 2021Article
- Zygotic Genome Activation: Critical Prelude to the Most Important Time of Your Life.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Epigenomic landscape of enhancer elements during Hydra head organizer formation.Epigenetics & chromatin · 2020Article
- A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.Developmental dynamics : an official publication of the American Association of Anatomists · 2019Article
- Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.Genome research · 2019Article
- Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules.Computational and structural biotechnology journal · 2019Article
- TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.BMC genomics · 2018Article
- Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis.Frontiers in cell and developmental biology · 2018Article
- ZIC3 in Heterotaxy.Advances in experimental medicine and biology · 2018Review
- Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.Developmental biology · 2017Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches--ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.