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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...editing site A become paired after editing, whereas only 4% of the paired A become unpaired after editing (Fig. 4C). To examine the impact of the editing on modulating sense miRNA targeting, we experimentally tested six miRNA-ATs in which the editing events altered predicted secondary structures and did...
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Research: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
- Yumeng Wang,
- Xiaoyan Xu,
- Shuangxing Yu,
- Kang Jin Jeong,
- Zhicheng Zhou,
- Leng Han,
- Yiu Huen Tsang,
- Jun Li,
- Hu Chen,
- Lingegowda S. Mangala,
- Yuan Yuan,
- A. Karina Eterovic,
- Yiling Lu,
- Anil K. Sood,
- Kenneth L. Scott,
- Gordon B. Mills,
- and Han Liang
Genome Res. July 2017 27: 1112-1125; Published in Advance April 14, 2017, doi:10.1101/gr.219741.116
...-type miR-200b expression. We further experimentally showed that, in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion andmigration through its impaired ability to inhibit ZEB1/ZEB2 and acquired concomitant ability to repress new targets, including LIFR, a well...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...as regulators by altering the number of RBP and miRNA binding sites. Furthermore, we identified potential sQTLs affecting the 3′ UTR length of the CD47 gene in sperm cells, which have a significant impact on reproductive traits. Cross-species analysis indicated that APA lengths are generally longer in brain...
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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
...a similarly modest reduction in miRNA levels in these libraries (Supplemental Fig. S2E; Supplemental Table S4). The comparable effect of dcr-1 RNAi on miRNAs, which are known Dicer substrates, and 23H-RNAs further supports a role for Dicer in 23H-RNA biogenesis (Grishok et al. 2001; Hutvágner et al. 2001...
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Resource: Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
- Bryan B. Teefy,
- Ari Adler,
- Alan Xu,
- Katelyn Hsu,
- Param Priya Singh,
- and Bérénice A. Benayoun
Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
...-interacting RNAs (piRNAs), which are complementary to or derived from TEs. piRNAs are expressed primarily in the gonad and are larger than miRNAs (Mani and Juliano 2013; Czech and Hannon 2016). Once bound to an RNA target, PIWI proteins cleave their target precisely 10 nt from the 5′ end of the complementary pi...
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Research: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
- Christine Roden,
- Jonathan Gaillard,
- Shaveta Kanoria,
- William Rennie,
- Syndi Barish,
- Jijun Cheng,
- Wen Pan,
- Jun Liu,
- Chris Cotsapas,
- Ye Ding,
- and Jun Lu
Genome Res. March 2017 27: 374-384; Published in Advance January 13, 2017, doi:10.1101/gr.208900.116
...and suggests a diverse impact of human genetic variation on miRNA biogenesis.Mature miRNAs are derived from hairpin-containing primary transcripts (pri-miRNAs). For the vast majority of miRNAs, pri-miRNAs are processed in the nucleus by the Microprocessor complex, containing DROSHA, DGCR8, and other proteins...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...transcriptase, and (RH) RNase H. Blue and red lines indicate primer binding sites (PBSs) and polypurine tracts (PPTs). The 21- to 22-nt small RNA (sRNA) data were obtained from a previous study (Creasey et al. 2014). Target positions of miRNAs are indicated as arrows (for details, see Supplemental Table S4...
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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
...were coupled with other features, including genomic organization, transcription rates, structural heterogeneity (isomiRs), and target abundance, measured through quantitative experimental approaches. This comprehensive analysis highlighted functional mechanisms that mediate miRNA degradation, as well...
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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
...). Then, we asked whether the deaminases that target tRNA also affect mRNA. Unlike in tRNA, there was no difference in the mRNA editing patterns between mutants and wild-type strains. Other types of RDDs were also unchanged in the deaminase mutants. The relative abundance of all 12 types is highly similar...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...of target mRNAs. For example, in mature B lymphocytes, a 3′ fragment derived from tRNAGlyGCC (referred to as 3′-tsRNAGlyGCC) has activities characteristic of a miRNA, including the capacity of binding to all four human AGOs and gene silencing via target sites in 3′ UTRs (Maute et al. 2013). In addition, ts...

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