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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
...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...cells and editing level analysis suggests that regulation of editing levels also depends on transcription.Eukaryotic gene expression of protein-coding genes involves transcription, RNA processing, RNA export, translation, and degradation of transcripts (Maniatis and Reed 2002; Keene 2007; Bentley 2014...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
...to post-transcriptional miRNA-dependent regulation, and the effects of DICER1 depletion are not restricted to cytoplasmic but extend to the nuclear APA fraction. This suggests direct and/or indirect effects of DICER1 on CPA site choice. Figure 5. miRNA-based stability plays a minimal role...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...that RDD formation is affected by mutations in genes regulating R-loops. Loss-of-function mutations in ribonuclease H, senataxin, and topoisomerase I that resolve RNA–DNA hybrids lead to increases in RDD frequency. Our results demonstrate that RDD is a conserved process that diversifies transcriptomes...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...that regulate different stages in a transcript’s life cycle. [Supplemental material is available for this article.] The 3′ ends of most RNA polymerase II–generated transcripts are generated through endonucleolytic cleavage and the addition of a polyadenosine tail of 70–100 nucleotides (nt) median length...
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Research: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
- Gabriel Kolle,
- Jill L. Shepherd,
- Brooke Gardiner,
- Karin S. Kassahn,
- Nicole Cloonan,
- David L.A. Wood,
- Ehsan Nourbakhsh,
- Darrin F. Taylor,
- Shivangi Wani,
- Hun S. Chy,
- Qi Zhou,
- Kevin McKernan,
- Scott Kuersten,
- Andrew L. Laslett,
- and Sean M. Grimmond
Genome Res. December 2011 21: 2014-2025; Published in Advance October 31, 2011, doi:10.1101/gr.119321.110
...; 4Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia Abstract Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...in a dedicated resource.Gene architecture in eukaryotes facilitates generation of more than one mRNA per gene through a differential combination of exons. The exonic region determination is under regulation of several co- and post-transcriptional mechanisms, in which alternative splicing (AS) plays a central...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...in addition to transcriptional or post-transcriptional RNA silencing. Levels of RNAi pathway proteins were relatively high compared to the proteome-wide distribution of label-free quantitation scores (Supplemental Fig. S4E). Proteins typically involved in sex and meiosis, as well as putative effectors, were...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...of the 5′ and 3′ UTRs of an mRNA molecule. UTRs play important roles in post-transcriptional regulation by containing sequence features that influence mRNA stability, localization, and translation efficiency (for review, see Di Giammartino et al. 2011). TSS usage delineates the 5′ UTR, which is involved...
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Research: Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
- Alina Chakraborty,
- Mandy Cadix,
- Sébastien Relier,
- Nicolò Taricco,
- Tina Alaeitabar,
- Alexandre Devaux,
- Céline M. Labbé,
- Sylvain Martineau,
- Amélie Heneman-Masurel,
- Pierre Gestraud,
- Alberto Inga,
- Nicolas Servant,
- Stéphan Vagner,
- and Martin Dutertre
Genome Res. July 2022 32: 1271-1284; Published in Advance July 20, 2022, doi:10.1101/gr.276192.121
...regulation of the IPA:LE isoform ratio across subcellular compartments during drug response and its coordination by an RNA-binding protein.The main pathway of eukaryotic pre-messenger RNA (pre-mRNA) 3′-end processing consists in transcript cleavage at the polyadenylation site, followed by the addition...

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