Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod
Abstract Background 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 depend...
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ftbiomed:oai:biomedcentral.com:1471-2164-13-443 2023-05-15T15:27:31+02:00 Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod Kleppe, Lene Edvardsen, Rolf B Kuhl, Heiner Malde, Ketil Furmanek, Tomasz Drivenes, Øyvind Reinhardt, Richard Taranger, Geir L Wargelius, Anna 2012-09-01 http://www.biomedcentral.com/1471-2164/13/443 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2164/13/443 Copyright 2012 Kleppe et al.; licensee BioMed Central Ltd. 3’UTR Sequence/EST filtering External spiking Transcriptome Teleost Embryonic development Research article 2012 ftbiomed 2012-10-06T23:55:20Z Abstract Background 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. Results 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. Conclusions 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. Article in Journal/Newspaper atlantic cod BioMed Central |
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collection |
BioMed Central |
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ftbiomed |
language |
English |
topic |
3’UTR Sequence/EST filtering External spiking Transcriptome Teleost Embryonic development |
spellingShingle |
3’UTR Sequence/EST filtering External spiking Transcriptome Teleost Embryonic development Kleppe, Lene Edvardsen, Rolf B Kuhl, Heiner Malde, Ketil Furmanek, Tomasz Drivenes, Øyvind Reinhardt, Richard Taranger, Geir L Wargelius, Anna Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
topic_facet |
3’UTR Sequence/EST filtering External spiking Transcriptome Teleost Embryonic development |
description |
Abstract Background 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. Results 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. Conclusions 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. |
format |
Article in Journal/Newspaper |
author |
Kleppe, Lene Edvardsen, Rolf B Kuhl, Heiner Malde, Ketil Furmanek, Tomasz Drivenes, Øyvind Reinhardt, Richard Taranger, Geir L Wargelius, Anna |
author_facet |
Kleppe, Lene Edvardsen, Rolf B Kuhl, Heiner Malde, Ketil Furmanek, Tomasz Drivenes, Øyvind Reinhardt, Richard Taranger, Geir L Wargelius, Anna |
author_sort |
Kleppe, Lene |
title |
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
title_short |
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
title_full |
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
title_fullStr |
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
title_full_unstemmed |
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod |
title_sort |
maternal 3’utrs: from egg to onset of zygotic transcription in atlantic cod |
publisher |
BioMed Central Ltd. |
publishDate |
2012 |
url |
http://www.biomedcentral.com/1471-2164/13/443 |
genre |
atlantic cod |
genre_facet |
atlantic cod |
op_relation |
http://www.biomedcentral.com/1471-2164/13/443 |
op_rights |
Copyright 2012 Kleppe et al.; licensee BioMed Central Ltd. |
_version_ |
1766357947353399296 |