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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...incorrectly annotated or always inefficiently spliced. Therefore, we conclude that zebrafish maternal mRNAs are fully spliced. Hnrnpa1 regulates poly(A) tail length and translation before ZGA through prominent 3′ UTR binding The abundance of hnRNP proteins in the preZGAmRBPome in the absence of unspliced...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...). Transcripts are often specified for decay through the binding of RNA and protein factors to cis-regulatory elements within the 3′ untranslated region (UTR) (Ray et al. 2013; Vejnar et al. 2019). Cross talk between factors can lead to differential mRNA decay, such as RNA-binding proteins stabilizing...
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Research: Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
- Håvard Aanes,
- Cecilia L. Winata,
- Chi Ho Lin,
- Jieqi P. Chen,
- Kandhadayar G. Srinivasan,
- Serene G.P. Lee,
- Adrian Y.M. Lim,
- Hajira Shreen Hajan,
- Philippe Collas,
- Guillaume Bourque,
- Zhiyuan Gong,
- Vladimir Korzh,
- Peter Aleström,
- and Sinnakaruppan Mathavan
Genome Res. August 2011 21: 1328-1338; Published in Advance May 9, 2011, doi:10.1101/gr.116012.110
...of maternal transcripts prior to MBT is critical for normal morphogenesis post-MBT. Cytoplasmic polyadenylation elements are found in the 39 UTR of pre-MBT transcripts It is generally accepted that regulation of polyadenylation is mediated through cis elements in the 39 UTR of mRNAs. We used programs provided...
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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
...structure (Fig. 3A,B).AU-rich elements in the 3′ UTR are positively correlated with the TIDindex (Fig. 3B; Supplemental Fig. S7C), further corroborating that this active mRNA decay pathway, mediated by specific RNA-binding proteins, mainly occurs in a translation-independent manner.Finally, although...
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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
...extensively used to study embryonic development (Howe et al. 2013). The first stage of zebrafish development is characterized by rapid cleavage of the embryonic cells and is entirely driven by the maternally provided mRNA and proteins as the zygotic is transcriptionally inactive until about 3 h post...
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Resource: The mRNA-bound proteome of the early fly embryo
- Hans-Hermann Wessels,
- Koshi Imami,
- Alexander G. Baltz,
- Marcin Kolinski,
- Anastasia Beldovskaya,
- Matthias Selbach,
- Stephen Small,
- Uwe Ohler,
- and Markus Landthaler
Genome Res. July 2016 26: 1000-1009; Published in Advance April 28, 2016, doi:10.1101/gr.200386.115
...-binding protein (RBP) Bruno (Kim-Ha et al. 1995; Castagnetti et al. 2000). This repression is relieved only after localization of the oskar mRNA to the posterior-most region of the embryo. Translation of oskar requires cis-acting RNA elements in its 3′ UTR (Kim-Ha et al. 1993), deposition of the exon junction...
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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for &gt;79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes...
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Research: Dynamic landscape of tandem 3′ UTRs during zebrafish development
- Yuxin Li,
- Yu Sun,
- Yonggui Fu,
- Mengzhen Li,
- Guangrui Huang,
- Chenxu Zhang,
- Jiahui Liang,
- Shengfeng Huang,
- Gaoyang Shen,
- Shaochun Yuan,
- Liangfu Chen,
- Shangwu Chen,
- and Anlong Xu
Genome Res. October 2012 22: 1899-1906; Published in Advance September 5, 2012, doi:10.1101/gr.128488.111
.... However, a positive correlation between the expression levels of the 39UTR isoforms and the number ofU-richmotifswas observed during this interval (Fig. 4E), suggesting that the 39 UTR isoforms with these U-rich elements are likely stabilized. High mRNA levels of the class-III ARE-binding protein elavl1...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...the RNA-induced silencing complex (RISC) and mediate gene silencing via binding to partially complementary elements in the 3′ untranslated region of target mRNAs, resulting in mRNA deadenylation and/or inhibition of translation (Bartel 2018). piRNAs are transcribed from hundreds of genomic clusters...
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Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
- Sanjana Pillay,
- Hazuki Takahashi,
- Piero Carninci,
- and Aditi Kanhere
Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
....tie1 is transcribed in zebrafish, mouse, and humans in the antisense direction to the tie1 gene (Li et al. 2010). Tie1 protein is a tyrosine kinase receptor for angioproteins and is essential for vascular development in vertebrates. The NAT, lnc.tie1, binds to tie1 mRNA through RNA:RNA hybridization...
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