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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
..., Isogai T, Suzuki Y, Akimitsu N. 2012. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res 22: 947–956. doi:10.1101/gr.130559.111 ↵Thomson DW, Bracken CP, Goodall GJ. 2011. Experimental strategies for microRNA target identification...
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Research: Genome-wide analysis of long noncoding RNA stability
- Michael B. Clark,
- Rebecca L. Johnston,
- Mario Inostroza-Ponta,
- Archa H. Fox,
- Ellen Fortini,
- Pablo Moscato,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
...Genome-wide analysis of long noncoding RNA stability Michael B. Clark 1 , Rebecca L. Johnston 1 , 5 , Mario Inostroza-Ponta 2 , Archa H. Fox 3 , Ellen Fortini 3 , Pablo Moscato 4 , Marcel E. Dinger 1 , 6 , 8...
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Research: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
- Shaofang Li,
- Lee E. Vandivier,
- Bin Tu,
- Lei Gao,
- So Youn Won,
- Shengben Li,
- Binglian Zheng,
- Brian D. Gregory,
- and Xuemei Chen
Genome Res. February 2015 25: 235-245; Published in Advance November 20, 2014, doi:10.1101/gr.182238.114
...Binglian Zheng Shaofang Li B Tu Brian D genome;gr.182238.114 1549-5469 10.1101/gr.182238.114 1088-9051 Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis Li et al. Genome-wide discovery of Pol IV/RDR2 products Research...
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Method: Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- Kentaro Kawata,
- Hiroyasu Wakida,
- Toshimichi Yamada,
- Kenzui Taniue,
- Han Han,
- Masahide Seki,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. October 2020 30: 1481-1491; Published in Advance August 25, 2020, doi:10.1101/gr.264408.120
...and degradation rates of genes are actually determined by the genes’ biological functions. A comparison of theoretical and experimental analyses revealed that the amount of RNA is determined by the ratio of RNA synthesis to degradation rates, whereas the rapidity of responses to external stimuli is determined...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...explanation for how short-lived, spatially restricted lncRNAs can exert long-range silencing effects.To mediate their long-range repressive effects in extraembryonic tissues and silence distal genes within their respective domains, Airn and Kcnq1ot1 recruit repressive histone-modifying complexes. Descriptive...
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Research: A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells
- Naoto Imamachi,
- Kazi Abdus Salam,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. March 2017 27: 407-418; Published in Advance December 9, 2016, doi:10.1101/gr.206060.116
...helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3′ untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify...
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Method: Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
- Matteo J. Marzi,
- Francesco Ghini,
- Benedetta Cerruti,
- Stefano de Pretis,
- Paola Bonetti,
- Chiara Giacomelli,
- Marcin M. Gorski,
- Theresia Kress,
- Mattia Pelizzola,
- Heiko Muller,
- Bruno Amati,
- and Francesco Nicassio
Genome Res. April 2016 26: 554-565; Published in Advance January 28, 2016, doi:10.1101/gr.198788.115
...rates at genome-wide scale in mammalian cells. Our analysis revealed heterogeneous miRNA half-lives, with many species behaving as stable molecules ( T 1/2 &gt; 24 h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over ( T 1/2 = 4–14 h). Decay rates...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...in decalcified FFPE conserved material (bone-related tissues), known to be incompatible with spatial transcriptomic assays because of RNA degradation. Finally, this technology has been used for performing spatial epigenomic profiling in mouse embryo samples, targeting several histone modifications assessed...
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Erratum: Errata Genome Res. July 2012 22: 1382

...genome;22/7/1382 1088-9051 Errata Errata Genome Research 22: 947–956 (2012) Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals Hidenori Tani, Rena Mizutani, Kazi Abdus Salam, Keiko Tano, Kenichi Ijiri, Ai Wakamatsu, Takao Isogai, Yutaka...

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