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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: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
...equally to this work. Corresponding authors: yangjh7@mail.sysu.edu.cn, lssqlh@mail.sysu.edu.cn, libin73@mail.sysu.edu.cn, tqyhe@email.jnu.edu.cnAbstractPolypeptides encoded by long noncoding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate...
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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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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: 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: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...is required to maintain pluripotency by regulating the PSN enhancer network via the recruitment of RNA polymerase II.Acetylation of lysine residues in histone tails is an essential post-translational modification (PTM), dynamically regulated by the opposing actions of histone acetyltransferases (HATs...
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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: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...of the newly identified proteins. This is in contrast to the generally low conservation observed for most of our novel genes (Fig. 3). This is consistent with evidence that loci encoding noncoding RNAs tend to evolve more rapidly than those encoding protein-coding genes (Necsulea et al. 2014). Analysis of our...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...author: rory.johnson@dbmr.unibe.chAbstractThe sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs...

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