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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
.... During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...are available, whereas commercial zebrafish anti-Ctcf antibodies are not available, requiring instead our procuring potential Ctcf binding sites by HOMER Motif finder across the Zv10 . We verified the presence of RNAs during ZGA encoding structural proteins (Ctcf and cohesin complex) and cohesin loading...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...) via the piRNA pathway (Watanabe et al. 2015), as well as promoter functions for ERVs that drive lncRNA expression (Davis et al. 2017; Gill et al. 2023). Our recent study demonstrated that ERVs function as active enhancers to drive expression of species-specific germline genes during the transition...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...in zebrafish are located on the long arm of Chromosome 4 (Chr 4q), a region previously noted for its enrichment in TEs, ZNFs, and immunity genes, as well as a wide variety of RNA-encoding loci (Howe et al. 2013, 2016). This physical colocalization of FZNFs superficially resembles that of KZNF genes, which form...
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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
...development and provide the basis for identifying mechanisms for this regulation.The developmental importance of mRNA degradation is underscored by the maternal-to-zygotic transition, in which maternal gene products in the early embryo must be degraded for the control of development to switch to zygotically...
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Research: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
- Guifen Liu,
- Wen Wang,
- Shengen Hu,
- Xiangxiu Wang,
- and Yong Zhang
Genome Res. July 2018 28: 998-1007; Published in Advance May 29, 2018, doi:10.1101/gr.228833.117
...to associate with a high methylation state were identified, including factors with high RNA levels during ZGA, such as Pou5f3 (the homolog of POU5F1 in zebrafish), Nanog, and Eomesa (Fig. 4B). The factor Eomesa is associated with endoderm formation (Bjornson et al. 2005), whereas Pou5f3 and Nanog are essential...
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Research: Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo
- Katharine N. Schulz,
- Eliana R. Bondra,
- Arbel Moshe,
- Jacqueline E. Villalta,
- Jason D. Lieb,
- Tommy Kaplan,
- Daniel J. McKay,
- and Melissa M. Harrison
Genome Res. November 2015 25: 1715-1726; Published in Advance September 2, 2015, doi:10.1101/gr.192682.115
...Lipshitz 2009). The degradation of maternally deposited mRNAs is coordinated with the transcriptional activation of the zygotic during the maternal-to-zygotic transition (MZT). This fundamental transition is conserved amongmetazoans and is essential for development. In Drosophila melanogaster, early development...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...hairpin precursors. MicroRNAs regulate gene expression by guiding the RNA-induced silencing complex (RISC) to complementary sites in the 3′ UTRs of target mRNAs, thereby inducing translational silencing and degradation (for review, see Bartel 2004). MicroRNA-target interaction usually requires base...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...embryos, whereas they are present in pre-ZGA mouse embryos (Xia et al. 2019). We thus reanalyzed the expression levels of writers, erasers, and related proteins of all histone modifications using our published RNA-seq data (Ichikawa et al. 2017; Nakamura et al. 2021), and confirmed their presence (at...
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Research: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
- Yujia Sun,
- Chung-Yi Nien,
- Kai Chen,
- Hsiao-Yun Liu,
- Jeff Johnston,
- Julia Zeitlinger,
- and Christine Rushlow
Genome Res. November 2015 25: 1703-1714; Published in Advance September 2, 2015, doi:10.1101/gr.192542.115
...and TF motifs are again occluded from TF access. Sun et al. 1710 Genome Research www..org heat-shocked during the second to third instar larval stage at 37°C for 1 h for 2 d. zld− embryos were depleted ofmaternal Zld through the “Maternal-Gal4-shRNA” system (Staller et al. 2013), where MTD-Gal4/UAS-shRNA...
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