Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
Open accessAbstract
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.
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In early zebrafish embryos, the relationship between poly(A)-tail length and tandem 3′-UTR isoform length is more pronounced when a predicted cytoplasmic polyadenylation element (CPE) is present in the unique region of the longer isoform.
“In early zebrafish embryos this relationship between 3′-UTR isoforms was even more pronounced when a predicted cytoplasmic polyadenylation element (CPE)4,19 was present in the unique region of the longer isoform (Extended Data Fig. 6b).”
From Poly(A)-tail profiling reveals an embryonic switch in translational control (2014) · cites this paper as [19]
Many mRNAs with short tails were observed in cleavage-stage embryos, consistent with known stability of short-tailed mRNAs in early embryos.
“Perhaps as a consequence, many mRNAs with short tails were observed (Fig. 2a), consistent with the known stability of short-tailed mRNAs in early embryos19,38.”
From Poly(A)-tail profiling reveals an embryonic switch in translational control (2014) · cites this paper as [19]
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Poly(A)-tail profiling reveals an embryonic switch in translational control
Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H., & Bartel, D. P. (2014) · Nature · doi:10.1038/nature13007 · Cited by 664 · see citing works
- Authors
- Aanes, H., Winata, C. L., Lin, C. H., Chen, J. P., Srinivasan, K. G., Lee, S. G. P., Lim, A. Y. M., Hajan, H. S., Collas, P., Bourque, G., Gong, Z., Korzh, V., Aleström, P., & Mathavan, S.
- Affiliations
- Norwegian University of Life Sciences (NO)
- Genome Institute of Singapore (SG)
- University of Oslo (NO)
- National University of Singapore (SG)
- Institute of Molecular and Cell Biology (SG)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-05-09
- Volume
- 21
- Issue
- 8
- Pages
- 1328-1338
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3149499
- OpenAlex
- W2161217765
- Cited by
- 285
- References
- 64
- Citations by year
- 2026: 12 · 2025: 11 · 2024: 11 · 2023: 7 · 2022: 10 · 2021: 16 · 2020: 14 · 2019: 22 · 2018: 20 · 2017: 25 · 2016: 27 · 2015: 22 · 2014: 33 · 2013: 29 · 2012: 17
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Genome Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Norges Forskningsråd
- Biomedical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- maternal-to-zygotic transition, midblastula transition, zebrafish, maternal transcripts, transcriptome dynamics, polyadenylation, early embryonic development, genome annotation, alternative splicing, splice variants, gene expression profiling
- MeSH terms
- Animals, Base Sequence, RNA, Messenger, Zebrafish, Zygote, Genome, Sequence Analysis, RNA, RNA, Messenger, Stored, Zebrafish Proteins, Transcriptome
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