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Functional annotation of human long noncoding RNAs via molecular phenotyping

Functional annotation of human long noncoding RNAs via molecular phenotyping
Functional annotation of human long noncoding RNAs via molecular phenotyping

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-to-date 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.

1088-9051
1060-1072
Ramilowski, Jordan A
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Yip, Chi Wai
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Agrawal, Saumya
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Chang, Jen-Chien
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Ciani, Yari
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Kulakovskiy, Ivan V
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Mendez, Mickaël
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Ooi, Jasmine Li Ching
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Ouyang, John F
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Parkinson, Nick
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Petri, Andreas
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Roos, Leonie
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Severin, Jessica
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Antonov, Ivan V
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Arner, Erik
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Bonetti, Alessandro
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Bono, Hidemasa
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Borsari, Beatrice
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Brombacher, Frank
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Cameron, Christopher JF
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Cannistraci, Carlo Vittorio
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Cardenas, Ryan
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Cardon, Melissa
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Chang, Howard
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Ducoli, Luca
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Favorov, Alexander
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Fort, Alexandre
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Garrido, Diego
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Gil, Noa
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Gimenez, Juliette
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Guler, Reto
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Handoko, Lusy
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Harshbarger, Jayson
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Heutink, Peter
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Hirose, Tetsuro
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Imada, Eddie L
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Itoh, Masayoshi
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Kaczkowski, Bogumil
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Kawaji, Hideya
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Kawashima, Tsugumi
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Kelly, S Thomas
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Kojima, Miki
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Kondo, Naoto
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Koseki, Haruhiko
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Kratz, Anton
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Kurowska-Stolarska, Mariola
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Kwon, Andrew Tae Jun
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Leek, Jeffrey
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Lennartsson, Andreas
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Lizio, Marina
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Luginbühl, Joachim
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Maeda, Shiori
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Makeev, Vsevolod J
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Marchionni, Luigi
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Medvedeva, Yulia A
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Minoda, Aki
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Müller, Ferenc
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Muñoz-Aguirre, Manuel
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Murata, Mitsuyoshi
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Nishiyori, Hiromi
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Nitta, Kazuhiro R
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Noguchi, Shuhei
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Nurtdinov, Ramil
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Okazaki, Yasushi
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Orlando, Valerio
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Paquette, Denis
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Parr, Callum J C
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Rackham, Owen J L
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Rizzu, Patrizia
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Sánchez Martinez, Diego Fernando
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Sandelin, Albin
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Sanjana, Pillay
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Shibayama, Youtaro
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Sivaraman, Divya M
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Suzuki, Takahiro
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Szumowski, Suzannah C
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Thongjuea, Supat
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Tripathi, Vidisha
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Ulitsky, Igor
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Verardo, Roberto
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Vorontsov, Ilya E
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Yamamoto, Chinatsu
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Young, Robert S
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Baillie, J Kenneth
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Forrest, Alistair R R
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Guigó, Roderic
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Hoffman, Michael M
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Hon, Chung Chau
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Kere, Juha
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Lenhard, Boris
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Schneider, Claudio
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Suzuki, Harukazu
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Yagi, Ken
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de Hoon, Michiel J L
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Shin, Jay W
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Carninci, Piero
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Ramilowski, Jordan A
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Yip, Chi Wai
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Agrawal, Saumya
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Chang, Jen-Chien
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Ciani, Yari
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Kulakovskiy, Ivan V
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Mendez, Mickaël
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Ooi, Jasmine Li Ching
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Ouyang, John F
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Roos, Leonie
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Arner, Erik
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Bonetti, Alessandro
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Bono, Hidemasa
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Borsari, Beatrice
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Brombacher, Frank
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Cardon, Melissa
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Chang, Howard
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Ducoli, Luca
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Favorov, Alexander
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Fort, Alexandre
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Gil, Noa
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Gimenez, Juliette
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Guler, Reto
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Handoko, Lusy
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Harshbarger, Jayson
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Kawashima, Tsugumi
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Kelly, S Thomas
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Kojima, Miki
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Kondo, Naoto
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Koseki, Haruhiko
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Kratz, Anton
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Kurowska-Stolarska, Mariola
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Kwon, Andrew Tae Jun
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Leek, Jeffrey
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Lennartsson, Andreas
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Luginbühl, Joachim
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Maeda, Shiori
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Makeev, Vsevolod J
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Marchionni, Luigi
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Medvedeva, Yulia A
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Murata, Mitsuyoshi
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Nishiyori, Hiromi
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Noguchi, Shuhei
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Nurtdinov, Ramil
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Okazaki, Yasushi
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Orlando, Valerio
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Paquette, Denis
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Rackham, Owen J L
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Rizzu, Patrizia
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Sánchez Martinez, Diego Fernando
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Sandelin, Albin
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Sanjana, Pillay
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Semple, Colin A M
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Shibayama, Youtaro
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Sivaraman, Divya M
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Thodberg, Malte
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Thongjuea, Supat
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Tripathi, Vidisha
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Ulitsky, Igor
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Verardo, Roberto
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Vorontsov, Ilya E
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Yamamoto, Chinatsu
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Young, Robert S
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Baillie, J Kenneth
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Forrest, Alistair R R
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Guigó, Roderic
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Hoffman, Michael M
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Hon, Chung Chau
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Kasukawa, Takeya
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Kauppinen, Sakari
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Kere, Juha
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Lenhard, Boris
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Schneider, Claudio
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Suzuki, Harukazu
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Yagi, Ken
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de Hoon, Michiel J L
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Shin, Jay W
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Carninci, Piero
8f5bcc38-0d65-4d67-9571-94f6409bd89d

Ramilowski, Jordan A, Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V, Mendez, Mickaël, 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, Christopher JF, 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, 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, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod J, Marchionni, Luigi, Medvedeva, Yulia A, Minoda, Aki, Müller, Ferenc, Muñoz-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, Sánchez Martinez, Diego Fernando, 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, 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 J L, Shin, Jay W and Carninci, Piero (2020) Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research, 30 (7), 1060-1072. (doi:10.1101/gr.254219.119).

Record type: Article

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-to-date 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.

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More information

Published date: July 2020
Additional Information: © 2020 Ramilowski et al.; Published by Cold Spring Harbor Laboratory Press.
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Identifiers

Local EPrints ID: 447700
URI: http://eprints.soton.ac.uk/id/eprint/447700
DOI: doi:10.1101/gr.254219.119
ISSN: 1088-9051
PURE UUID: 8ed0f828-1862-453c-95de-42f5e39c12ab
ORCID for Owen J L Rackham: ORCID iD orcid.org/0000-0002-4390-0872

Catalogue record

Date deposited: 18 Mar 2021 17:46
Last modified: 17 Mar 2024 04:03

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Contributors

Author: Jordan A Ramilowski
Author: Chi Wai Yip
Author: Saumya Agrawal
Author: Jen-Chien Chang
Author: Yari Ciani
Author: Ivan V Kulakovskiy
Author: Mickaël Mendez
Author: Jasmine Li Ching Ooi
Author: John F Ouyang
Author: Nick Parkinson
Author: Andreas Petri
Author: Leonie Roos
Author: Jessica Severin
Author: Kayoko Yasuzawa
Author: Imad Abugessaisa
Author: Altuna Akalin
Author: Ivan V Antonov
Author: Erik Arner
Author: Alessandro Bonetti
Author: Hidemasa Bono
Author: Beatrice Borsari
Author: Frank Brombacher
Author: Christopher JF Cameron
Author: Carlo Vittorio Cannistraci
Author: Ryan Cardenas
Author: Melissa Cardon
Author: Howard Chang
Author: Josée Dostie
Author: Luca Ducoli
Author: Alexander Favorov
Author: Alexandre Fort
Author: Diego Garrido
Author: Noa Gil
Author: Juliette Gimenez
Author: Reto Guler
Author: Lusy Handoko
Author: Jayson Harshbarger
Author: Akira Hasegawa
Author: Yuki Hasegawa
Author: Kosuke Hashimoto
Author: Norihito Hayatsu
Author: Peter Heutink
Author: Tetsuro Hirose
Author: Eddie L Imada
Author: Masayoshi Itoh
Author: Bogumil Kaczkowski
Author: Aditi Kanhere
Author: Emily Kawabata
Author: Hideya Kawaji
Author: Tsugumi Kawashima
Author: S Thomas Kelly
Author: Miki Kojima
Author: Naoto Kondo
Author: Haruhiko Koseki
Author: Tsukasa Kouno
Author: Anton Kratz
Author: Mariola Kurowska-Stolarska
Author: Andrew Tae Jun Kwon
Author: Jeffrey Leek
Author: Andreas Lennartsson
Author: Marina Lizio
Author: Fernando López-Redondo
Author: Joachim Luginbühl
Author: Shiori Maeda
Author: Vsevolod J Makeev
Author: Luigi Marchionni
Author: Yulia A Medvedeva
Author: Aki Minoda
Author: Ferenc Müller
Author: Manuel Muñoz-Aguirre
Author: Mitsuyoshi Murata
Author: Hiromi Nishiyori
Author: Kazuhiro R Nitta
Author: Shuhei Noguchi
Author: Yukihiko Noro
Author: Ramil Nurtdinov
Author: Yasushi Okazaki
Author: Valerio Orlando
Author: Denis Paquette
Author: Callum J C Parr
Author: Owen J L Rackham ORCID iD
Author: Patrizia Rizzu
Author: Diego Fernando Sánchez Martinez
Author: Albin Sandelin
Author: Pillay Sanjana
Author: Colin A M Semple
Author: Youtaro Shibayama
Author: Divya M Sivaraman
Author: Takahiro Suzuki
Author: Suzannah C Szumowski
Author: Michihira Tagami
Author: Martin S Taylor
Author: Chikashi Terao
Author: Malte Thodberg
Author: Supat Thongjuea
Author: Vidisha Tripathi
Author: Igor Ulitsky
Author: Roberto Verardo
Author: Ilya E Vorontsov
Author: Chinatsu Yamamoto
Author: Robert S Young
Author: J Kenneth Baillie
Author: Alistair R R Forrest
Author: Roderic Guigó
Author: Michael M Hoffman
Author: Chung Chau Hon
Author: Takeya Kasukawa
Author: Sakari Kauppinen
Author: Juha Kere
Author: Boris Lenhard
Author: Claudio Schneider
Author: Harukazu Suzuki
Author: Ken Yagi
Author: Michiel J L de Hoon
Author: Jay W Shin
Author: Piero Carninci

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