Functional annotation of human long noncoding RNAs via molecular phenotyping
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Ramilowski , J A , Yip , C W , Agrawal , S , Chang , J-C , Ciani , Y , Kulakovskiy , I V , Mendez , M , Ooi , J L C , Ouyang , J F , Parkinson , N , Petri , A , Roos , L , Severin , J , Yasuzawa , K , Abugessaisa , I , Akalin , A , Antonov , I V , Arner , E , Bonetti , A , Bono , H , Borsari , B , Brombacher , F , Cameron , C J F , Cannistraci , C V , Cardenas , R , Cardon , M , Chang , H , Dostie , J , Ducoli , L , Favorov , A , Fort , A , Garrido , D , Gil , N , Gimenez , J , Guler , R , Handoko , L , Harshbarger , J , Hasegawa , A , Hasegawa , Y , Hashimoto , K , Hayatsu , N , Heutink , P , Hirose , T , Imada , E L , Itoh , M , Kaczkowski , B , Kanhere , A , Kawabata , E , Kawaji , H , Kawashima , T , Kelly , S T , Kojima , M , Kondo , N , Koseki , H , Kouno , T , Kratz , A , Kurowska-Stolarska , M , Kwon , A T J , Leek , J , Lennartsson , A , Lizio , M , Lopez-Redondo , F , Luginbuhl , J , Maeda , S , Makeev , V J , Marchionni , L , Medvedeva , Y A , Minoda , A , Mueller , F , Munoz-Aguirre , M , Murata , M , Nishiyori , H , Nitta , K R , Noguchi , S , Noro , Y , Nurtdinov , R , Okazaki , Y , Orlando , V , Paquette , D , Parr , C J C , Rackham , O J L , Rizzu , P , Martinez , D F S , Sandelin , A , Sanjana , P , Semple , C A M , Shibayama , Y , Sivaraman , D M , Suzuki , T , Szumowski , S C , Tagami , M , Taylor , M S , Terao , C , Thodberg , M , Thongjuea , S , Tripathi , V , Ulitsky , I , Verardo , R , Vorontsov , I E , Yamamoto , C , Young , R S , Baillie , J K , Forrest , A R R , Guigo , R , Hoffman , M M , Hon , C C , Kasukawa , T , Kauppinen , S , Kere , J , Lenhard , B , Schneider , C , Suzuki , H , Yagi , K , Hoon , M J L D , Shin , J W & Carninci , P 2020 , ' Functional annotation of human long noncoding RNAs via molecular phenotyping ' , Genome Research , vol. 30 , no. 7 , pp. 1060-1072 . https://doi.org/10.1101/gr.254219.119
| Title: | Functional annotation of human long noncoding RNAs via molecular phenotyping |
| Author: | Ramilowski, Jordan A.; Yip, Chi Wai; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan V.; Mendez, Mickael; Ooi, Jasmine Li Ching; Ouyang, John F.; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Brombacher, Frank; Cameron, Chris J. F.; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josee; Ducoli, Luca; Favorov, Alexander; Fort, Alexandre; Garrido, Diego; Gil, Noa; Gimenez, Juliette; Guler, Reto; Handoko, Lusy; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Kosuke; Hayatsu, Norihito; Heutink, Peter; Hirose, Tetsuro; Imada, Eddie L.; Itoh, Masayoshi; Kaczkowski, Bogumil; Kanhere, Aditi; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S. Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; Lopez-Redondo, Fernando; Luginbuhl, Joachim; Maeda, Shiori; Makeev, Vsevolod J.; Marchionni, Luigi; Medvedeva, Yulia A.; Minoda, Aki; Mueller, Ferenc; Munoz-Aguirre, Manuel; Murata, Mitsuyoshi; Nishiyori, Hiromi; Nitta, Kazuhiro R.; Noguchi, Shuhei; Noro, Yukihiko; Nurtdinov, Ramil; Okazaki, Yasushi; Orlando, Valerio; Paquette, Denis; Parr, Callum J. C.; Rackham, Owen J. L.; Rizzu, Patrizia; Martinez, Diego Fernando Sanchez; Sandelin, Albin; Sanjana, Pillay; Semple, Colin A. M.; Shibayama, Youtaro; Sivaraman, Divya M.; Suzuki, Takahiro; Szumowski, Suzannah C.; Tagami, Michihira; Taylor, Martin S.; Terao, Chikashi; Thodberg, Malte; Thongjuea, Supat; Tripathi, Vidisha; Ulitsky, Igor; Verardo, Roberto; Vorontsov, Ilya E.; Yamamoto, Chinatsu; Young, Robert S.; Baillie, J. Kenneth; Forrest, Alistair R. R.; Guigo, Roderic; Hoffman, Michael M.; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; Hoon, Michiel J. L. de; Shin, Jay W.; Carninci, Piero |
| Contributor organization: | STEMM - Stem Cells and Metabolism Research Program Juha Kere / Principal Investigator Research Programs Unit University of Helsinki HUS Helsinki and Uusimaa Hospital District |
| Date: | 2020-07 |
| Language: | eng |
| Number of pages: | 13 |
| Belongs to series: | Genome Research |
| ISSN: | 1088-9051 |
| DOI: | https://doi.org/10.1101/gr.254219.119 |
| URI: | http://hdl.handle.net/10138/319237 |
| Abstract: | Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. 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 exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-todate lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2. |
| Subject: |
ADULT HUMAN FIBROBLASTS
GENE-EXPRESSION UNIQUE FEATURES CELLS TRANSCRIPTION REVEALS DIFFERENTIATION TRANSLATION PRINCIPLES REGULATORS 3111 Biomedicine 1182 Biochemistry, cell and molecular biology 318 Medical biotechnology 1184 Genetics, developmental biology, physiology |
| Peer reviewed: | Yes |
| Rights: | cc_by |
| Usage restriction: | openAccess |
| Self-archived version: | publishedVersion |
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Articles from TUHAT CRIS [52329]