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

Matthew P Davis,Anton J Enright,Derek L Stemple,John E Collins,Zsofia Digby,Anja Füllgrabe,Neha Wali,Elisabeth M Busch-Nentwich,Thibaut Hourlier,Konstantinos Billis,Daniel N Murphy,Ian M Sealy,Richard J White,Christopher M Dooley

doi:10.7554/elife.30860

Matthew P Davis, Anton J Enright + Show 12 more

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https://doi.org/10.7554/elife.30860

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Abstract

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.

Highlights

Gene regulatory interactions are the fundamental basis of embryonic development and transcription is one of the major processes by which these interactions are mediated
A time-resolved comprehensive analysis of relative mRNA expression levels is an important step towards understanding the regulatory processes governing embryonic development
Together with a high quality genome (Howe et al, 2013b) only comparable in vertebrates to mouse and human, this has led to many important discoveries in areas such as zygotic genome activation (ZGA; Lee et al, 2013), blood stem cell biology (Bertrand et al, 2010; Kissa and Herbomel, 2010), and findings directly affecting human health (Li et al, 2015; Tobin et al, 2010)

Summary

Introduction

Gene regulatory interactions are the fundamental basis of embryonic development and transcription is one of the major processes by which these interactions are mediated. The zebrafish is a unique vertebrate model system as it possesses high morphological and genomic conservation with humans, and experimental tractability of embryogenesis otherwise only found in invertebrate model organisms such as Drosophila melanogaster or Caenorhabditis elegans Features such as very large numbers of offspring, ex vivo development and embryonic translucency have enabled comprehensive forward and reverse genetic screens (Amsterdam et al, 1999; Driever et al, 1996; Haffter et al, 1996; Kettleborough et al, 2013; Moens et al, 2008; Varshney et al, 2015) as well as high-throughput drug discovery approaches (Murphey et al, 2006; North et al, 2007; Peterson et al, 2000; Peterson et al, 2004; Stern et al, 2005). Together with a high quality genome (Howe et al, 2013b) only comparable in vertebrates to mouse and human, this has led to many important discoveries in areas such as zygotic genome activation (ZGA; Lee et al, 2013), blood stem cell biology (Bertrand et al, 2010; Kissa and Herbomel, 2010), and findings directly affecting human health (Li et al, 2015; Tobin et al, 2010)

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