Functional annotation of human long noncoding RNAs via molecular phenotyping

Show full item record



Permalink

http://hdl.handle.net/10138/319237

Citation

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
Other contributor: University of Helsinki, STEMM - Stem Cells and Metabolism Research Program



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
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
Genome_Res._2020_Ramilowski_1060_72.pdf 8.728Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record