title: Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.
abstract: 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.
authors.affiliation: BasAM, Norwegian School of Veterinary Science, 0033 Oslo, Norway.
authors.forename: Håvard
authors.initials: H
authors.lastname: Aanes
authors.forename: Cecilia L
authors.initials: CL
authors.lastname: Winata
authors.forename: Chi Ho
authors.initials: CH
authors.lastname: Lin
authors.forename: Jieqi P
authors.initials: JP
authors.lastname: Chen
authors.forename: Kandhadayar G
authors.initials: KG
authors.lastname: Srinivasan
authors.forename: Serene G P
authors.initials: SG
authors.lastname: Lee
authors.forename: Adrian Y M
authors.initials: AY
authors.lastname: Lim
authors.forename: Hajira Shreen
authors.initials: HS
authors.lastname: Hajan
authors.forename: Philippe
authors.initials: P
authors.lastname: Collas
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Gong
authors.forename: Vladimir
authors.initials: V
authors.lastname: Korzh
authors.forename: Peter
authors.initials: P
authors.lastname: Aleström
authors.forename: Sinnakaruppan
authors.initials: S
authors.lastname: Mathavan
mesh_terms: D000818:Animals; D001483:Base Sequence; D016678:Genome; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D023121:RNA, Messenger, Stored / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism; D015053:Zygote / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D023121:RNA, Messenger, Stored; D029961:Zebrafish Proteins