Functional characterization of the zebrafish genes requires accurate knowledge of the gene structure and gene expression. In proposal we combine high-throughput sequencing techniques (Ribosome profile and RNA-seq) and bioinformatics to improve the current annotation of coding and non-coding genes, by determining the translation start and stop sites in each coding gene (Aim 2), define the transcription start site, 5'and 3'UTRs (Aim 1), annotate putative alternatively spliced exons in the zebrafish genes (Aim 1), and develop a gene expression atlas during embryogenesis and organogenesis (Aim 1) The experiments outlined in this proposal have the ultimate goal of improving functional genomics in zebrafish and will provide two fundamental tools to the community: i) improved annotation of the zebrafish genes including coding potential, translation start site and transcript structure and ii) community defined, open access zebrafish expression atlas across embryonic/ larval stages and organogenesis. In the future, the results derived from this project will facilitate the functional characterization of the zebrafish genes and will establsh a frame work to understand the structure and the function of vertebrate genes.

Public Health Relevance

The genome of vertebrate animals is very similar to that of humans. By studying the secrets underlying in the genetic code of the vertebrate model system zebrafish, we aim to characterize the elements of the genome to provide better tools to zebrafish researchers to understand vertebrate development and human disease. The experiments outlined in this proposal will also help us uncover novel genes unknown in humans providing important insights about the building blocks that are used in humans to undertake different functions in the cell.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Coulombe, James N
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Yale University
Schools of Medicine
New Haven
United States
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Fernandez, Juan Pablo; Moreno-Mateos, Miguel Angel; Gohr, Andre et al. (2018) RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet 14:e1007473
White, Richard J; Collins, John E; Sealy, Ian M et al. (2017) A high-resolution mRNA expression time course of embryonic development in zebrafish. Elife 6:
Yartseva, Valeria; Takacs, Carter M; Vejnar, Charles E et al. (2017) RESA identifies mRNA-regulatory sequences at high resolution. Nat Methods 14:201-207
Moreno-Mateos, Miguel A; Fernandez, Juan P; Rouet, Romain et al. (2017) CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Commun 8:2024
Bazzini, Ariel A; Del Viso, Florencia; Moreno-Mateos, Miguel A et al. (2016) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 35:2087-2103
Hoffman, Ellen J; Turner, Katherine J; Fernandez, Joseph M et al. (2016) Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron 89:725-33
Pignatelli, Miguel; Vilella, Albert J; Muffato, Matthieu et al. (2016) ncRNA orthologies in the vertebrate lineage. Database (Oxford) 2016:
Yates, Andrew; Akanni, Wasiu; Amode, M Ridwan et al. (2016) Ensembl 2016. Nucleic Acids Res 44:D710-6
Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel et al. (2016) The Ensembl gene annotation system. Database (Oxford) 2016:
Johnstone, Timothy G; Bazzini, Ariel A; Giraldez, Antonio J (2016) Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J 35:706-23

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