ArticleNucleic acids research2005
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
51 citing papers in PubMed, 87 citations in OpenAlex.
- Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution.Genome biology and evolution · 2024Article
- Cis-regulatory control of mammalian Trps1 gene expression.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2024Article
- Zebrafish-An Optimal Model in Experimental Oncology.Molecules (Basel, Switzerland) · 2022Review
- Distinctive functional regime of endogenous lncRNAs in dark regions of human genome.Computational and structural biotechnology journal · 2022Article
- Heart Enhancers: Development and Disease Control at a Distance.Frontiers in genetics · 2021Review
- Functional Analysis of Two NovelMicroorganisms · 2020Article
- Species-Specific in vitro and in vivo Evaluation of Toxicity of Silver Nanoparticles Stabilized with Gum Arabic Protein.International journal of nanomedicine · 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
- A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human.Nucleic acids research · 2018Article
- Article
- Differential Toxicity of mDia Formin-Directed Functional Agonists and Antagonists in Developing Zebrafish.Frontiers in pharmacology · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Cardiac Light-Sheet Fluorescent Microscopy for Multi-Scale and Rapid Imaging of Architecture and Function.Scientific reports · 2016Article
- Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.Genome biology and evolution · 2014Article
- Harnessing mobile genetic elements to explore gene regulation.Mobile genetic elements · 2014Review
- Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.PloS one · 2014Article
- Enhancer turnover and conserved regulatory function in vertebrate evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- Evolution of transcriptional enhancers and animal diversity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.Nucleic acids research · 2013Article
- Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Whole genome comparisons of distantly related species effectively predict biologically important sequences--core genes and cis-acting regulatory elements (REs)--but require experimentation to verify biological activity. To examine the efficacy of comparative genomics in identification of active REs from anonymous, non-coding (NC) sequences, we generated a novel alignment of the human and draft zebrafish genomes, and contrasted this set to existing human and fugu datasets. We tested the transcriptional regulatory potential of candidate sequences using two in vivo assays. Strict selection of non-genic elements which are deeply conserved in vertebrate evolution identifies 1744 core vertebrate REs in human and two fish genomes. We tested 16 elements in vivo for cis-acting gene regulatory properties using zebrafish transient transgenesis and found that 10 (63%) strongly modulate tissue-specific expression of a green fluorescent protein reporter vector. We also report a novel quantitative enhancer assay with potential for increased throughput based on normalized luciferase activity in vivo. This complementary system identified 11 (69%; including 9 of 10 GFP-confirmed elements) with cis-acting function. Together, these data support the utility of comparative genomics of distantly related vertebrate species to identify REs and provide a scaleable, in vivo quantitative assay to define functional activity of candidate REs.
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Registered trials
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.