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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
...in such translation regulation with a developmental context, we performed Ribo-seq for estimating gene-specific TE. As detailed above for our analysis in Figure 4C, we similarly divided the predicted target genes of pupa-accumulated tsRNAs into three functional groups (metamorphosis, translation, and others). Figure...
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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
.... As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs...
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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
...in the stems, the 5′-most G is completely conserved within all Class I RNAs from all six dictyostelids representing each evolutionary group of Dictyostelia. The predicted base-paired structure of the stem and the unstructured feature of the conserved sequence motif correspond well with previous in vitro...
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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
...Yak, droEre)), droAna), (droPer, droPse)), droWil), ((droVir, droMoj), droGri)) (Stark et al. 2007). All lncRNAs emerging more than 40 million years ago were regarded as old lncRNAs (Chen et al. 2010), and the young lncRNAs were further divided into two or three age groups to calculate the relative...
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Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...to predict the silencing class of all unlabeled X-linked genes given the same set of input features. The predictions are validated by comparing them to measured half-times from undifferentiated mRNA-seq data, with pyrosequencing experiments (few selected genes) and with measured silencing dynamics of genes...
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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
..., none of the 230 nat-siRNA-associated NAT pairs were regulated by light. These results suggest that natsiRNA-mediated regulation of NAT pairs does not contribute to light signaling pathways in general. Discussion Long noncoding NATs are a pervasive feature of the Arabidopsis The proportion of antisense...
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Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- Stefan Washietl,
- Manolis Kellis,
- and Manuel Garber
Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
...gene annotations in human (Derrien et al. 2012). We based our analysis on version 12 of GENCODE, which includes 30,645 noncoding transcripts grouped in 11,790 loci. This set includes transcript types that overlap protein-coding genes such as intronic noncoding RNAs or noncoding isoforms of mRNAs...
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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...). As observed in previous studies (Chen et al. 2005; RIKEN Genome Exploration Research Group et al. 2005), the expression of most SAS gene pairs was positively correlated, indicating concordant expression (Fig. 2A). Regions of SAS overlap are enriched in exons with antisense-correlated splicing events RNA...
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Resource: Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
- Andrea Pauli,
- Eivind Valen,
- Michael F. Lin,
- Manuel Garber,
- Nadine L. Vastenhouw,
- Joshua Z. Levin,
- Lin Fan,
- Albin Sandelin,
- John L. Rinn,
- Aviv Regev,
- and Alexander F. Schier
Genome Res. March 2012 22: 577-591; Published in Advance November 22, 2011, doi:10.1101/gr.133009.111
...intergenic, 184 intronic overlapping, and 566 antisense exonic overlapping transcripts, many of which are expressed in a developmentally regulatedmanner.We characterized each lncRNA by diverse features, including transcript structure, evolutionary conservation, developmental expression, and associated...
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Research: Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications
- Artur Veloso,
- Killeen S. Kirkconnell,
- Brian Magnuson,
- Benjamin Biewen,
- Michelle T. Paulsen,
- Thomas E. Wilson,
- and Mats Ljungman
Genome Res. June 2014 24: 896-905; Published in Advance April 8, 2014, doi:10.1101/gr.171405.113
...Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications Artur Veloso 1 , 2 , Killeen S. Kirkconnell 1 , 3 , Brian Magnuson 1 , Benjamin Biewen 1 , 4 , Michelle T. Paulsen 1...

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