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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
...that poly(A)-selected RNA sequencing is not an accurate reflection of true mRNA levels before ZGA. (B) FZNF expression from rRNA-depleted reads, before ZGA. (C) Maternally deposited genes are significantly older, whereas early-stage FZNFs are young and generally unique to D. rerio. Ages were quantified...
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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
...decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3′ UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...the localization (Bullock et al. 2010), splicing (Buratti and Baralle 2004), and translation (Ding et al. 2014) of mRNAs. As a result, secondary structure influences nearly every processing step in the life cycle of transcripts (Vandivier et al. 2016).Secondary structures can have another effect: They act...
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Research: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
- Deni Subasic,
- Anneke Brümmer,
- Yibo Wu,
- Sérgio Morgado Pinto,
- Jochen Imig,
- Martin Keller,
- Marko Jovanovic,
- Helen Louise Lightfoot,
- Sara Nasso,
- Sandra Goetze,
- Erich Brunner,
- Jonathan Hall,
- Ruedi Aebersold,
- Mihaela Zavolan,
- and Michael O. Hengartner
Genome Res. November 2015 25: 1680-1691; Published in Advance July 31, 2015, doi:10.1101/gr.183160.114
...and protein expression levels following the dismantling of the most abundant C. elegans miRNA family, which indicate that miR-58 family members exert both translation inhibition and mRNA degradation on their targets, with eventual mRNA degradation being the dominant consequence of miRNA repression. Results...
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Research: microRNA target prediction programs predict many false positives
- Natalia Pinzón,
- Blaise Li,
- Laura Martinez,
- Anna Sergeeva,
- Jessy Presumey,
- Florence Apparailly,
- and Hervé Seitz
Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
....] Together with a protein member of the Argonaute family, microRNAs (miRNAs) constitute the RNA-induced silencing complex (RISC), which represses specific mRNA targets by translation inhibition and mRNA decay (Iwakawa and Tomari 2015). Target recognition is typically mediated by imperfect base...
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Research: TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network
- Jonathan Krell,
- Justin Stebbing,
- Claudia Carissimi,
- Aleksandra F. Dabrowska,
- Alexander de Giorgio,
- Adam E. Frampton,
- Victoria Harding,
- Valerio Fulci,
- Giuseppe Macino,
- Teresa Colombo,
- and Leandro Castellano
Genome Res. March 2016 26: 331-341; Published in Advance December 23, 2015, doi:10.1101/gr.191759.115
...that refining our knowledge of their roles in TP53-signaling networks and their gene targets is crucial to achieving a greater understanding of tumorigenesis. Importantly, miRNAs only become active regulators of their mRNA targets once they interact with AGO1-4 proteins, the key components of the RNA...
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Research: Signatures of RNA binding proteins globally coupled to effective microRNA target sites
- Anders Jacobsen,
- Jiayu Wen,
- Debora S. Marks,
- and Anders Krogh
Genome Res. August 2010 20: 1010-1019; Published in Advance May 27, 2010, doi:10.1101/gr.103259.109
...changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting may be modulated by other mRNA sequence elements such as binding sites for the hundreds of RNA binding proteins (RNA-BPs) expressed in any cell, and this aspect has not been...
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Letter: Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets
- Jean Hausser,
- Markus Landthaler,
- Lukasz Jaskiewicz,
- Dimos Gaidatzis,
- and Mihaela Zavolan
Genome Res. November 2009 19: 2009-2020; Published in Advance September 18, 2009, doi:10.1101/gr.091181.109
...of zebrafish by DND1 protein (Kedde et al. 2007)—involve interactions of U-rich elements, and a study of mRNA decay (Yang et al. 2003) also identified a number of AU-rich elements that positively correlated with degradation rate. Consistent with the nucleotide bias, the energy required to open the secondary...
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Research: Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements
- Joanne L. Harding,
- Stuart Horswell,
- Claire Heliot,
- Javier Armisen,
- Lyle B. Zimmerman,
- Nicholas M. Luscombe,
- Eric A. Miska,
- and Caroline S. Hill
Genome Res. January 2014 24: 96-106; Published in Advance September 24, 2013, doi:10.1101/gr.144469.112
...RNAs that are experimentally detectable in frogs, mice, and humans. By combining the small RNA sequencing with mRNA profiling at the different developmental stages, we identify a new class of small noncoding RNAs that we name siteRNAs, which align in clusters to introns of protein-coding genes. We show that site...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...al. 2000; Bernstein et al. 2001; Elbashir et al. 2001; Grishok et al. 2001; Ketting et al. 2001; Knight and Bass 2001). Argonaute proteins associate with siRNA duplexes, discarding one strand and retaining the other, which then acts as a guide to direct silencing of target messenger RNAs (mRNAs...

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