A high-resolution mRNA expression time course of embryonic development in zebrafish

• Published in: eLife Vol. 6
• Main Authors: White, Richard J, Collins, John E, Sealy, Ian M, Wali, Neha, Dooley, Christopher M, Digby, Zsofia, Stemple, Derek L, Murphy, Daniel N, Billis, Konstantinos, Hourlier, Thibaut, Füllgrabe, Anja, Davis, Matthew P, Enright, Anton J, Busch-Nentwich, Elisabeth M
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 16-11-2017; eLife Sciences Publications, Ltd
• Subjects: Animals; Annotations; Chromosome 4; Danio rerio; Datasets; Developmental Biology; Embryogenesis; Embryonic Development; Exons; Fertilization; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genetic engineering; Genetics and Genomics; Genomes; miRNA; Morphology; Poly(A); Proteins; RNA, Messenger - biosynthesis; RNA-seq; Sequence Analysis, RNA; Time Factors; Tools and Resources; Transcription; transcriptome; Zebrafish; Zebrafish - embryology; Zinc finger proteins; stem cells; embryogenesis; evolutionary biology; RNA-seq; developmental biology; transcriptome; genomics; zebrafish
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.30860

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3' ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.