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; Piero Carninci

doi:10.1101/gr.254219.119

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Functional annotation of human long noncoding RNAs via molecular phenotyping

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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, …

Genome research, Vol.30(7), pp.1060-1072

01/07/2020

DOI: https://doi.org/10.1101/gr.254219.119

PMCID: 7397864

PMID: 32718982

Abstract

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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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Title: Functional annotation of human long noncoding RNAs via molecular phenotyping
Creators - without role: Jordan A. Ramilowski - RIKEN Center for Integrative Medical Sciences
Chi Wai Yip - RIKEN Center for Integrative Medical Sciences
Saumya Agrawal - RIKEN Center for Integrative Medical Sciences
Jen-Chien Chang - RIKEN Center for Integrative Medical Sciences
Yari Ciani - Consorzio Interuniversitario per le Biotecnologie
Ivan V. Kulakovskiy - Engelhardt Institute of Molecular Biology
Mickaël Mendez - University of Toronto
Jasmine Li Ching Ooi
John F. Ouyang - National University of Singapore
Nick Parkinson - University of Edinburgh
Andreas Petri - Aalborg University
Leonie Roos - MRC London Institute of Medical Sciences
Jessica Severin - RIKEN Center for Integrative Medical Sciences
Kayoko Yasuzawa - RIKEN Center for Integrative Medical Sciences
Imad Abugessaisa - RIKEN Center for Integrative Medical Sciences
Altuna Akalin - Max Delbrück Center for Molecular Medicine
Ivan V. Antonov - Russian Academy of Sciences
Erik Arner
Alessandro Bonetti
Hidemasa Bono - Hiroshima University
Beatrice Borsari - Centre for Genomic Regulation
Frank Brombacher - International Centre for Genetic Engineering and Biotechnology
Christopher J.F. Cameron - McGill University
Carlo Vittorio Cannistraci - Center for Systems Biology Dresden
Ryan Cardenas - University of Birmingham
Melissa Cardon - RIKEN Center for Integrative Medical Sciences
Howard Chang - Stanford University
Josée Dostie - McGill University
Luca Ducoli - École Polytechnique Fédérale de Lausanne
Alexander Favorov - Vavilov Institute of General Genetics
Alexandre Fort
Diego Garrido - Centre for Genomic Regulation
Noa Gil - Weizmann Institute of Science
Juliette Gimenez - Fondazione Santa Lucia
Reto Guler - International Centre for Genetic Engineering and Biotechnology
Lusy Handoko
Jayson Harshbarger
Akira Hasegawa - RIKEN Center for Integrative Medical Sciences
Yuki Hasegawa
Kosuke Hashimoto - RIKEN Center for Integrative Medical Sciences
Norihito Hayatsu - RIKEN Center for Integrative Medical Sciences
Peter Heutink - German Center for Neurodegenerative Diseases
Tetsuro Hirose - Osaka University
Eddie L. Imada - Johns Hopkins University
Masayoshi Itoh
Bogumil Kaczkowski - RIKEN Center for Integrative Medical Sciences
Aditi Kanhere - University of Birmingham
Emily Kawabata
Hideya Kawaji
Tsugumi Kawashima - RIKEN Center for Integrative Medical Sciences
S. Thomas Kelly - RIKEN Center for Integrative Medical Sciences
Miki Kojima - RIKEN Center for Integrative Medical Sciences
Naoto Kondo
Haruhiko Koseki - RIKEN Center for Integrative Medical Sciences
Tsukasa Kouno - RIKEN Center for Integrative Medical Sciences
Anton Kratz
Mariola Kurowska-Stolarska - University of Glasgow
Andrew Tae Jun Kwon - RIKEN Center for Integrative Medical Sciences
Jeffrey Leek - Johns Hopkins University
Andreas Lennartsson - Karolinska Institutet
Marina Lizio - RIKEN Center for Integrative Medical Sciences
Fernando López-Redondo - RIKEN Center for Integrative Medical Sciences
Joachim Luginbühl - RIKEN Center for Integrative Medical Sciences
Shiori Maeda - RIKEN Center for Integrative Medical Sciences
Vsevolod J. Makeev - Vavilov Institute of General Genetics
Luigi Marchionni - Johns Hopkins University
Yulia A. Medvedeva - Russian Academy of Sciences
Aki Minoda - RIKEN Center for Integrative Medical Sciences
Ferenc Müller - University of Birmingham
Manuel Muñoz-Aguirre - Centre for Genomic Regulation
Mitsuyoshi Murata - RIKEN Center for Integrative Medical Sciences
Hiromi Nishiyori - RIKEN Center for Integrative Medical Sciences
Kazuhiro R. Nitta - RIKEN Center for Integrative Medical Sciences
Shuhei Noguchi - RIKEN Center for Integrative Medical Sciences
Yukihiko Noro
Ramil Nurtdinov - Centre for Genomic Regulation
Yasushi Okazaki - RIKEN Center for Integrative Medical Sciences
Valerio Orlando - King Abdullah University of Science and Technology
Denis Paquette - McGill University
Callum J.C. Parr
Owen J.L. Rackham - Duke-NUS Medical School
Patrizia Rizzu - German Center for Neurodegenerative Diseases
Diego Fernando Sánchez Martinez
Albin Sandelin - University of Copenhagen
Pillay Sanjana - University of Birmingham
Colin A.M. Semple - MRC Institute of Genetics and Molecular Medicine
Youtaro Shibayama - RIKEN Center for Integrative Medical Sciences
Divya M. Sivaraman - RIKEN Center for Integrative Medical Sciences
Takahiro Suzuki
Suzannah C. Szumowski
Michihira Tagami - RIKEN Center for Integrative Medical Sciences
Martin S. Taylor - University of Edinburgh
Chikashi Terao - RIKEN Center for Integrative Medical Sciences
Malte Thodberg - University of Copenhagen
Supat Thongjuea
Vidisha Tripathi - National Centre for Cell Science
Igor Ulitsky - Weizmann Institute of Science
Roberto Verardo - Consorzio Interuniversitario per le Biotecnologie
Ilya E. Vorontsov - Vavilov Institute of General Genetics
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
Piero Carninci
Publication Details: Genome research, Vol.30(7), pp.1060-1072
Publisher: Cold Spring Harbor Laboratory Press
Grant note: ; P30 CA006973 / ; R01CA200859; W81XWH-16-1-0739 / NIH National Cancer Institute 18-14-00240 / ; RIKEN Center for Integrative Medical Sciences (IMS) Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement (Generalitat de Catalunya) Swedish Cancer Society 18-34-20024; 2017FI_B00722 / ; 20298 / Versus Arthritis UK RIKEN Special Post-Doctoral Research (SPDR) 0112-2019-0001 / ; APP1154524 / Australian National Health and Medical Research Council Fellowship RGPIN-2015-3948; CMPT177780 / ; Swedish Research Council, the Swedish Childhood Cancer fund Novo Nordisk Foundation, Lundbeck Foundation, Danish Cancer Society, Carlsberg Foundation, Independent Research Fund Denmark RIKEN Center for Life Science Technology, Division of Genomic Technologies (CLST DGT) 17-00-00208; LCF/BQ/SO15/52260001 / ;
Identifiers: 9941733708331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article