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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...; Kristensen et al. 2022). To name a few, circBIRC6 has been found to play a role in cell pluripotency (Yu et al. 2017); circHIPK3, in cell growth (Zheng et al. 2016); and circular Foxo3, in suppression of cancer cell proliferation and survival (Yang et al. 2016). Because of its circular structure, circRNAs...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...of the structure–function relationship in lncRNAs.The discovery of long noncoding RNAs (lncRNAs) has revolutionized scientific understanding of the and has led to an explosion of research into the complex mechanisms that regulate gene expression. Currently, lncRNAs are broadly defined as any RNA >200 nt in length...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...Present address: AstraZeneca Discovery Sciences, Translational Genomics, 43183 Mölndal, Sweden Corresponding author: michiel.dehoon@riken.jpAbstractIn eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs...
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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 Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China; 4Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China Corresponding authors: jun_ma@zju.edu.cn, feng_he@zju.edu.cnAbstractA class of noncoding RNAs...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...in this paper, in-network miRNAs are likely to contribute to dormancy entry via other events such as suppression of cell cycle and cellular growth. In line with this, PCNA (regulator of cell proliferation) and RIF1 (regulator of replication timing) are down-regulated, among others, in our network. Depletion...
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Resource: Functional annotation of human long noncoding RNAs via molecular phenotyping
- Jordan A. Ramilowski,
- Chi Wai Yip,
- Saumya Agrawal,
- Jen-Chien Chang,
- Yari Ciani,
- Ivan V. Kulakovskiy,
- Mickaël Mendez,
- Jasmine Li Ching Ooi,
- John F. Ouyang,
- Nick Parkinson,
- Andreas Petri,
- Leonie Roos,
- Jessica Severin,
- Kayoko Yasuzawa,
- Imad Abugessaisa,
- Altuna Akalin,
- Ivan V. Antonov,
- Erik Arner,
- Alessandro Bonetti,
- Hidemasa Bono,
- Beatrice Borsari,
- Frank Brombacher,
- Christopher J.F. Cameron,
- Carlo Vittorio Cannistraci,
- Ryan Cardenas,
- Melissa Cardon,
- Howard Chang,
- Josée Dostie,
- Luca Ducoli,
- Alexander Favorov,
- Alexandre Fort,
- Diego Garrido,
- Noa Gil,
- Juliette Gimenez,
- Reto Guler,
- Lusy Handoko,
- Jayson Harshbarger,
- Akira Hasegawa,
- Yuki Hasegawa,
- Kosuke Hashimoto,
- Norihito Hayatsu,
- Peter Heutink,
- Tetsuro Hirose,
- Eddie L. Imada,
- Masayoshi Itoh,
- Bogumil Kaczkowski,
- Aditi Kanhere,
- Emily Kawabata,
- Hideya Kawaji,
- Tsugumi Kawashima,
- S. Thomas Kelly,
- Miki Kojima,
- Naoto Kondo,
- Haruhiko Koseki,
- Tsukasa Kouno,
- Anton Kratz,
- Mariola Kurowska-Stolarska,
- Andrew Tae Jun Kwon,
- Jeffrey Leek,
- Andreas Lennartsson,
- Marina Lizio,
- Fernando López-Redondo,
- Joachim Luginbühl,
- Shiori Maeda,
- Vsevolod J. Makeev,
- Luigi Marchionni,
- Yulia A. Medvedeva,
- Aki Minoda,
- Ferenc Müller,
- Manuel Muñoz-Aguirre,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Kazuhiro R. Nitta,
- Shuhei Noguchi,
- Yukihiko Noro,
- Ramil Nurtdinov,
- Yasushi Okazaki,
- Valerio Orlando,
- Denis Paquette,
- Callum J.C. Parr,
- Owen J.L. Rackham,
- Patrizia Rizzu,
- Diego Fernando Sánchez Martinez,
- Albin Sandelin,
- Pillay Sanjana,
- Colin A.M. Semple,
- Youtaro Shibayama,
- Divya M. Sivaraman,
- Takahiro Suzuki,
- Suzannah C. Szumowski,
- Michihira Tagami,
- Martin S. Taylor,
- Chikashi Terao,
- Malte Thodberg,
- Supat Thongjuea,
- Vidisha Tripathi,
- Igor Ulitsky,
- Roberto Verardo,
- Ilya E. Vorontsov,
- Chinatsu Yamamoto,
- Robert S. Young,
- J. Kenneth Baillie,
- Alistair R.R. Forrest,
- Roderic Guigó,
- Michael M. Hoffman,
- Chung Chau Hon,
- Takeya Kasukawa,
- Sakari Kauppinen,
- Juha Kere,
- Boris Lenhard,
- Claudio Schneider,
- Harukazu Suzuki,
- Ken Yagi,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- and Piero Carninci
Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
..., Connecticut 06510, USA ↵47 These authors contributed equally to this work. Corresponding authors: michiel.dehoon@riken.jp, jay.shin@riken.jp, carninci@riken.jpAbstractLong noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian s, and yet, their functions remain largely unknown...
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Research: Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas
- Jonas Kjellin,
- Lotta Avesson,
- Johan Reimegård,
- Zhen Liao,
- Ludwig Eichinger,
- Angelika Noegel,
- Gernot Glöckner,
- Pauline Schaap,
- and Fredrik Söderbom
Genome Res. March 2021 31: 436-447; Published in Advance January 21, 2021, doi:10.1101/gr.272856.120
..., Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal...
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Method: Quantifying full-length circular RNAs in cancer
- Ken Hung-On Yu,
- Christina Huan Shi,
- Bo Wang,
- Savio Ho-Chit Chow,
- Grace Tin-Yun Chung,
- Raymond Wai-Ming Lung,
- Ke-En Tan,
- Yat-Yuen Lim,
- Anna Chi-Man Tsang,
- Kwok-Wai Lo,
- and Kevin Y. Yip
Genome Res. December 2021 31: 2340-2353; Published in Advance October 18, 2021, doi:10.1101/gr.275348.121
...(Kristensen et al. 2018). Some of them have been shown to play oncogenic (Guarnerio et al. 2016) or tumor-suppressive (Li et al. 2015) roles. Because circRNAs are relatively stable compared with their linear counterparts owing to their resistance to RNA exonuclease (Memczak et al. 2013), they can potentially...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China ↵3 These authors contributed equally to this work. Corresponding authors: songwei@ibms.pumc.edu.cn, j-yu@ibms.pumc.edu.cn, yanni_ma@126.comAbstractLong noncoding RNAs (lncRNAs) have...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...of neighboring genes, and thus function via a cis-acting mechanism (Lee and Bartolomei 2013; Mercer and Mattick 2013). LncRNAs have also been proposed to regulate gene expression in trans; examples include the TP53-induced lncRNAsDlx6os1 and Hotair (Feng et al. 2006; Huarte et al. 2010; Chu et al. 2011). However...

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