Zebrafish mRNA sequencing decipher novelties in transcriptome dynamics during maternal to zygotic transition

Abstract

It is generally accepted that maternally deposited mRNAs direct early development before zygotic transcription initiation during mid-blastula transition. To study mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (oocyte to early gastrulation) stages. The genome-wide transcriptome analysis documented at least 5000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined the expression levels of maternal and zygotic transcripts with highest resolution possible using mRNA-seq, and clustered them based on their expression pattern. We discovered a novel phenomenon of delayed polyadenylation in a large cohort of maternal transcripts during pre-MBT stage of the embryos, for the first time in zebrafish, and suggest a major role of this process in regulating developmental events linked to the mid-blastula transition. Our study identified a large number of novel transcribed regions in un-annotated regions of the genome which will facilitate re-annotation of the zebrafish genome. We also identified splice variants during early zebrafish embryogenesis with an estimated frequency of 40-75%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish early developmental events.