The zebrafish transcriptome during early development

Abstract

BackgroundThe transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized. In this study RNA-Seq is used to compare the transcription profiles of four early developmental stages in zebrafish (Danio rerio) on a global scale.ResultsAn average of 79 M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187, of which 10096 were present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. The sequence data (accession number ERP000635) is available at the European Nucleotide Archive.ConclusionClustering of expression profiles shows that a majority of the detected gene transcripts are present at steady levels, and thus a minority of the gene transcripts clusters as increasing or decreasing in expression over the four investigated developmental stages. The three earliest developmental stages were similar when comparing highly expressed genes, whereas the 50% epiboly stage differed from the other three stages in the identity of highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions. Taken together, these observations indicate a major transition in gene regulation and transcriptional activity taking place between the 512-cell and 50% epiboly stages, in accordance with previous studies.

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

“…Compared to two recent RNA-seq-based transcriptome studies in zebrafish embryos (Aanes et al 2011;Vesterlund et al 2011), our data set is of significantly higher depth: a total of about 220 million (Vesterlund et al 2011) and about 100 million (Aanes et al 2011) mapped reads from four and six embryonic stages, respectively, versus about 1.5 billion mapped reads in our study (Supplemental Table 1). Moreover, we identify many more known and novel transcribed loci: about 4000 ''novel transcribed regions'' reported by Vesterlund et al (2011) and Aanes et al (2011) versus more than 9000 novel loci in our embryonic transcriptome with no previous annotations in RefSeq or Ensembl.…”

“…We recovered the vast majority of expressed RefSeq transcripts, identified thousands of novel expressed loci and novel isoforms, and also captured the dynamic changes in expression levels of each transcript as development proceeds. Our data set is of about threeto fourfold higher depth than two recent zebrafish RNA-seq studies (Aanes et al 2011;Vesterlund et al 2011). This higher sequencing depth also translated into a significant increase in the number of identified expressed genes and was particularly important for the detection of lncRNAs that are expressed at relatively low levels.…”

“…Moreover, we identify many more known and novel transcribed loci: about 4000 ''novel transcribed regions'' reported by Vesterlund et al (2011) and Aanes et al (2011) versus more than 9000 novel loci in our embryonic transcriptome with no previous annotations in RefSeq or Ensembl. This suggests that our embryonic transcriptome provides a highly comprehensive and more complete assembly than that previously available.…”

“…As a measure of quality of our data set, we were able to reconstruct the vast majority of annotated zebrafish RefSeq genes and a large fraction of Ensembl gene models (Flicek et al 2011). In contrast to recent smaller-scale RNA-seq studies that focused on protein-coding genes (Aanes et al 2011;Vesterlund et al 2011), we annotated and analyzed lncRNAs at high temporal resolution. We combined RNA-seq-based de novo transcript identification with a stringent filtering of putative protein-coding transcripts to define a high-confidence set of 1133 multi-exonic noncoding transcripts.…”

Advances in genomics for flatfish aquaculture

“…RNA-seq can evaluate the complete set of transcripts in a given species in one sample, including mRNAs, their splicing and gene boundaries, ncRNAs and small RNAs, such as microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and small nucleolar (snoRNAs) as well as small interfering (siRNAs) RNAs. Although most RNA-seq analyses in fish have been applied to gene discovery, identification of splice variants and quantification of gene expression (Meijer et al 2005;Aanes et al 2011;Coppe et al 2010;Fu et al 2011;Vesterlund et al 2011;Zhang et al 2011b), other applications such as SNP identification (Canovas et al 2010;Yang et al 2011), allele-specific gene expression (Degner et al 2009), or interaction transcriptome-epigenome (Elling and Deng 2009), are also possible and will probably be explored in the near future. As mentioned earlier, most farmed fish lack a reference genome and in most cases the transcriptome information available is very scarce.…”