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    Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

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    Type
    Preprint
    Authors
    Ramilowski, Jordan
    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
    Arner, Erik
    Bonetti, Alessandro
    Bono, Hidemasa cc
    Borsari, Beatrice
    Brombacher, Frank
    Cannistraci, Carlo Vittorio
    Cardenas, Ryan
    Cardon, Melissa
    Chang, Howard
    Dostie, Josée
    Ducoli, Luca
    Favorov, Alexander
    Fort, Alexandre
    Garrido, Diego
    Gil, Noa
    Gimenez, Juliette
    Guler, Reto
    Handoko, Lusy
    Harshbarger, Jayson
    Hasegawa, Akira
    Hasegawa, Yuki
    Hashimoto, Kosuke cc
    Hayatsu, Norihito
    Heutink, Peter
    Hirose, Tetsuro
    Imada, Eddie L
    Itoh, Masayoshi
    Kaczkowski, Bogumil
    Kanhere, Aditi
    Kawabata, Emily
    Kawaji, Hideya
    Kawashima, Tsugumi
    Kelly, Tom
    Kojima, Miki
    Kondo, Naoto
    Koseki, Haruhiko
    Kouno, Tsukasa
    Kratz, Anton
    Kurowska-Stolarska, Mariola
    Kwon, Andrew Tae Jun
    Leek, Jeffrey
    Lennartsson, Andreas
    Lizio, Marina
    Lopez, Fernando
    Luginbühl, Joachim
    Maeda, Shiori
    Makeev, Vsevolod
    Marchionni, Luigi
    Medvedeva, Yulia A
    Minoda, Aki
    Müller, Ferenc
    Aguirre, Manuel Munoz
    Murata, Mitsuyoshi
    Nishiyori, Hiromi
    Nitta, Kazuhiro
    Noguchi, Shuhei
    Noro, Yukihiko
    Nurtdinov, Ramil
    Okazaki, Yasushi
    Orlando, Valerio cc
    Paquette, Denis
    Parr, Callum
    Rackham, Owen JL
    Rizzu, Patrizia
    Sanchez, Diego Fernando
    Sandelin, Albin
    Sanjana, Pillay
    Semple, Colin AM
    Sharma, Harshita
    Shibayama, Youtaro
    Sivaraman, Divya
    Suzuki, Takahiro
    Szumowski, Suzannah
    Tagami, Michihira
    Taylor, Martin S
    Terao, Chikashi
    Thodberg, Malte
    Thongjuea, Supat
    Tripathi, Vidisha
    Ulitsky, Igor cc
    Verardo, Roberto
    Vorontsov, Ilya
    Yamamoto, Chinatsu
    Young, Robert S
    Baillie, J Kenneth cc
    Forrest, Alistair RR
    Guigó, Roderic
    Hoffman, Michael M
    Hon, Chung Chau
    Kasukawa, Takeya
    Kauppinen, Sakari
    Kere, Juha
    Lenhard, Boris
    Schneider, Claudio
    Suzuki, Harukazu
    Yagi, Ken
    de Hoon, Michiel
    Shin, Jay W
    Carninci, Piero cc
    FANTOM consortium
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Date
    2019-07-16
    Permanent link to this record
    http://hdl.handle.net/10754/660473
    
    Metadata
    Show full item record
    Abstract
    Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). The resulting transcriptomic profiles recapitulated the observed cellular phenotypes, yielding specific roles for over 40% of analyzed lncRNAs in regulating distinct biological pathways, transcriptional machinery, alternative promoter activity and architecture usage. Overall, combining cellular and molecular profiling provided a powerful approach to unravel the distinct functions of lncRNAs, which we highlight with specific functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
    Citation
    Ramilowski, J., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., … Parkinson, N. (2019). Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. doi:10.1101/700864
    Publisher
    Cold Spring Harbor Laboratory
    DOI
    10.1101/700864
    Additional Links
    http://biorxiv.org/lookup/doi/10.1101/700864
    https://www.biorxiv.org/content/biorxiv/early/2019/07/18/700864.full.pdf
    ae974a485f413a2113503eed53cd6c53
    10.1101/700864
    Scopus Count
    Collections
    Biological and Environmental Sciences and Engineering (BESE) Division; Preprints; Bioscience Program

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