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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...). TE 5mC in all contexts is lower in Spirodela compared to Arabidopsis, with very low mCHG levels and hardly any mCHH (Fig. 1C). This is in agreement with the partial dependency of mCHH on 24 nt siRNAs. In addition, Spirodela lacks gene body CG methylation (gbM) (Supplemental Fig. S4A; Michael et al...
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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
....ricci@ens-lyon.org, melissa.moore@umassmed.eduAbstractmRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific...
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Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
- Charlie Y. Shi,
- Lara E. Elcavage,
- Raghu R. Chivukula,
- Joanna Stefano,
- Benjamin Kleaveland,
- and David P. Bartel
Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
...influence of ZSWIM8, and presumably TDMD, in mammalian biology is widespread and consequential, and posit the existence of many yet-unidentified transcripts that trigger miRNA degradation.MicroRNAs (miRNAs) are ∼22-nucleotide (nt) RNAs that associate with Argonaute (AGO) proteins to guide the repression...
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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
...and protecting transcripts from miRNA-mediated repression (Bhattacharyya et al. 2006; Young et al. 2012). Furthermore, computational analyses predict widespread antagonistic or synergistic actions between RNA-binding proteins and miRNAs in regulating gene expression (Jiang et al. 2013). Translational efficiency...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...of action driven exclusively by transcript cleavage. This finding is in line with proposals that most plant miRNAs repress their targets using both transcript cleavage and TR (Brodersen et al. 2008; Li et al. 2013a; Yu et al. 2017) and indeed lead us to posit that TR is widespread in miRNA-dependent...
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Research: Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis
- Marija Petrić Howe,
- Hamish Crerar,
- Jacob Neeves,
- Jasmine Harley,
- Giulia E. Tyzack,
- Pierre Klein,
- Andres Ramos,
- Rickie Patani,
- and Raphaëlle Luisier
Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
...in mammalian systems and for a long time was mostly considered as a product of inefficient or erroneous splicing. With advances in detection strategies, IR is now recognized as a more widespread and regulated process than previously thought, and the idea that IR could even functionally modulate cellular...
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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
...transcripts. Comparison with Drosophila shows that microRNA-mediated maternal transcript targeting is a conserved process in insects, but the number and sequences of microRNAs involved have diverged. The expression of fast-evolving and species-specific microRNAs in the early blastoderm of T. castaneum...
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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
.... Short sequences provide limited information on how the sequence context influences regulation by individual motifs, whereas longer sequences lack resolution to pinpoint distinct segments driving regulation. To address these issues, we recently developed a high-throughput RNA-element selection assay...
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Research: Exonic splice regulation imposes strong selection at synonymous sites
- Rosina Savisaar and
- Laurence D. Hurst
Genome Res. October 2018 28: 1442-1454; Published in Advance August 24, 2018, doi:10.1101/gr.233999.117
....001) (Supplemental Fig. S1; Supplemental Table S3). This initial analysis suggests that ∼30% of ESE motif occurrences are functional. Importantly, this method may overestimate conservation levels by about a third because it does not control for context-dependent mutational biases (Supplemental Text S2). A more...
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Research: LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- Jan Attig,
- George R. Young,
- Louise Hosie,
- David Perkins,
- Vesela Encheva-Yokoya,
- Jonathan P. Stoye,
- Ambrosius P. Snijders,
- Nicola Ternette,
- and George Kassiotis
Genome Res. October 2019 29: 1578-1590; Published in Advance September 19, 2019, doi:10.1101/gr.248922.119
...). MicroRNA-mediated down-regulation of HECTD2 expression has been proposed to drive androgen independence in prostate cancer (Sun et al. 2014), and more recently, HECTD2 copy number alterations were suggested as drivers in neuroblastoma patients (Suo et al. 2018). However, the function of HECTD2 in cancer...
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