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

2011; Cold Spring Harbor Laboratory Press; Volume: 21; Issue: 8 Linguagem: Inglês

10.1101/gr.116012.110

1549-5469

Håvard Aanes, Cecilia Lanny Winata, Chi Ho Lin, Jieqi P. Chen, Kandhadayar G. Srinivasan, Serene G.P. Lee, Adrian Yin Ming Lim, Hajira Shreen Hajan, Philippe Collas, Guillaume Bourque, Zhiyuan Gong, Vladimir Korzh, Peter Aleström, Sinnakaruppan Mathavan,

Cancer-related molecular mechanisms research

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50%-60%. 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.