ArticleNucleic acids research2013
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Article
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.Nature communications · 2026Article
- Harnessing population genetics and animal models to uncover the genetics of skin scarring.Journal of plastic, reconstructive & aesthetic surgery : JPRAS · 2026Review
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.bioRxiv : the preprint server for biology · 2025Article
- Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development.Nucleic acids research · 2024Article
- Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.Genome biology and evolution · 2024Article
- Hypoxia-induced immortalization of primary cells depends on Tfcp2L1 expression.Cell death & disease · 2024Article
- Essential role of PLD2 in hypoxia-induced stemness and therapy resistance in ovarian tumors.Journal of experimental & clinical cancer research : CR · 2024Article
- Activator-blocker model of transcriptional regulation by pioneer-like factors.Nature communications · 2023Article
- Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state.The Journal of clinical investigation · 2023Article
- Article
- Prevalent Introgression Underlies Convergent Evolution in the Diversification of Pungitius Sticklebacks.Molecular biology and evolution · 2023Article
- A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish.Cell genomics · 2022Article
- Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers.Nature communications · 2022Article
- Gain of gene regulatory network interconnectivity at the origin of vertebrates.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate.Science advances · 2022Article
- Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration.Development (Cambridge, England) · 2022Article
- Pluripotency factors determine gene expression repertoire at zygotic genome activation.Nature communications · 2022Article
- Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics.Scientific reports · 2021Article
- CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.Nature communications · 2021Article
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7 authors.
Funding
Abstract
Many important model organisms for biomedical and evolutionary research have sequenced genomes, but occupy a phylogenetically isolated position, evolutionarily distant from other sequenced genomes. This phylogenetic isolation is exemplified for zebrafish, a vertebrate model for cis-regulation, development and human disease, whose evolutionary distance to all other currently sequenced fish exceeds the distance between human and chicken. Such large distances make it difficult to align genomes and use them for comparative analysis beyond gene-focused questions. In particular, detecting conserved non-genic elements (CNEs) as promising cis-regulatory elements with biological importance is challenging. Here, we develop a general comparative genomics framework to align isolated genomes and to comprehensively detect CNEs. Our approach integrates highly sensitive and quality-controlled local alignments and uses alignment transitivity and ancestral reconstruction to bridge large evolutionary distances. We apply our framework to zebrafish and demonstrate substantially improved CNE detection and quality compared with previous sets. Our zebrafish CNE set comprises 54 533 CNEs, of which 11 792 (22%) are conserved to human or mouse. Our zebrafish CNEs (http://zebrafish.stanford.edu) are highly enriched in known enhancers and extend existing experimental (ChIP-Seq) sets. The same framework can now be applied to the isolated genomes of frog, amphioxus, Caenorhabditis elegans and many others.
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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.