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Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod

Lene Kleppe1*, Rolf B Edvardsen1, Heiner Kuhl2, Ketil Malde1, Tomasz Furmanek1, Øyvind Drivenes1, Richard Reinhardt3, Geir L Taranger1 and Anna Wargelius1

Author affiliations

1 Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway

2 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195, Berlin-Dahlem, Germany

3 Max-Planck Genome centre, MPI fuer Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-80829, Koeln, Germany

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Citation and License

BMC Genomics 2012, 13:443  doi:10.1186/1471-2164-13-443

Published: 1 September 2012



Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Atlantic cod egg and embryo viability is variable, and it is hypothesized that the early development depends upon the feature of these maternal RNAs. Both the length and the presence of specific motifs in the 3’UTR of maternal RNAs are believed to regulate expression and stability of the maternal transcripts. Therefore, the aim of this study was to characterize the overall composition and 3’UTR structure of the most common maternal RNAs found in cod eggs and pre-zygotic embryos.


22229 Sanger-sequences were obtained from 3’-end sequenced cDNA libraries prepared from oocyte, 1-2 cell, blastula and gastrula stages. Quantitative PCR revealed that EST copy number below 9 did not reflect the gene expression profile. Consequently genes represented by less than 9 ESTs were excluded from downstream analyses, in addition to sequences with low-quality gene hits. This provided 12764 EST sequences, encoding 257 unique genes, for further analysis. Mitochondrial transcripts accounted for 45.9-50.6% of the transcripts isolated from the maternal stages, but only 12.2% of those present at the onset of zygotic transcription. 3’UTR length was predicted in nuclear sequences with poly-A tail, which identified 191 3’UTRs. Their characteristics indicated a more complex regulation of transcripts that are abundant prior to the onset of zygotic transcription. Maternal and stable transcripts had longer 3’UTR (mean 187.1 and 208.8 bp) and more 3’UTR isoforms (45.7 and 34.6%) compared to zygotic transcripts, where 15.4% had 3’UTR isoforms and the mean 3’UTR length was 76 bp. Also, diversity and the amount of putative polyadenylation motifs were higher in both maternal and stable transcripts.


We report on the most pronounced processes in the maternally transferred cod transcriptome. Maternal stages are characterized by a rich abundance of mitochondrial transcripts. Maternal and stable transcripts display longer 3'UTRs with more variation of both polyadenylation motifs and 3'UTR isoforms. These data suggest that cod eggs possess a complex array of maternal RNAs which likely act to tightly regulate early developmental processes in the newly fertilized egg.

3’UTR; Sequence/EST filtering; External spiking; Transcriptome; Teleost; Embryonic development