17 Andersson, Robin Gebhard, Claudia Miguel-Escalada, Irene Hoof, Ilka Bornholdt, Jette Boyd, Mette Chen, Yun Zhao, Xiaobei Schmidl, Christian Suzuki, Takahiro Ntini, Evgenia Arner, Erik Valen, Eivind Li, Kang Schwarzfischer, Lucia Glatz, Dagmar Raithel, Johanna Lilje, Berit Rapin, Nicolas Bagger, Frederik Otzen Jørgensen, Mette Andersen, Peter Refsing Bertin, Nicolas Rackham, Owen Burroughs, A Maxwell Baillie, J Kenneth Ishizu, Yuri Shimizu, Yuri Furuhata, Erina Maeda, Shiori Negishi, Yutaka Mungall, Christopher J Meehan, Terrence F Lassmann, Timo Itoh, Masayoshi Kawaji, Hideya Kondo, Naoto Kawai, Jun Lennartsson, Andreas Daub, Carsten O Heutink, Peter Hume, David A Jensen, Torben Heick Suzuki, Harukazu Hayashizaki, Yoshihide Müller, Ferenc Forrest, Alistair R R Carninci, Piero Rehli, Michael Sandelin, Albin Forrest, Alistair R R Kawaji, Hideya Rehli, Michael Baillie, J Kenneth de Hoon, Michiel J L Haberle, Vanja Lassmann, Timo Kulakovskiy, Ivan V Lizio, Marina Itoh, Masayoshi Andersson, Robin Mungall, Christoher J Meehan, Terrence F Schmeier, Sebastian Bertin, Nicolas Jørgensen, Mette Dimont, Emmanuel Arner, Erik Schmid, Christian Schaefer, Ulf Medvedeva, Yulia A Plessy, Charles Vitezic, Morana Severin, James Semple, Colin A Ishizu, Yuri Young, Robert S Francescatto, Margherita Alam, Intikhab Albanese, Davide Altschuler, Gabriel M Arakawa, Takahiro Archer, John A C Arner, Peter Babina, Magda Rennie, Sarah Balwierz, Piotr J Beckhouse, Anthony G Pradhan-Bhatt, Swati Blake, Judith A Blumenthal, Antje Bodega, Beatrice Bonetti, Alessandro Briggs, James Brombacher, Frank Burroughs, A Maxwell Califano, Andrea Cannistracti, Carlo V Carbajo, Daniel Chen, Yun Chierici, Marco Ciani, Yari Clevers, Hans C Dalla, Emiliano Davis, Carrie A Detmar, Michael Diehl, Alexander D Dohi, Taeko Drabløs, Finn Edge, Albert S B Edinger, Matthias Ekwall, Karl Endoh, Mitsuhiro Enomoto, Hideki Fagiolini, Michela Fairbairn, Lynsey Fang, Hai Farach-Carson, Mary C Faulkner, Geoffrey J 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Haruhiko Koyasu, Shigeo Krampitz, Sarah Kubosaki, Atsutaka Kwon, Andrew T Laros, Jeroen F J Lee, Weonju Lennartsson, Andreas Li, Kang Lilje, Berit Lipovich, Leonard Mackay-Sim, Alan Manabe, Ri-ichiroh Mar, Jessica C Marchand, Benoit Mathelier, Anthony Mejhert, Niklas Meynert, Alison Mizuno, Yosuke de Lima Morais, David A Morikawa, Hiromasa Morimoto, Mitsuru Moro, Kazuyo Motakis, Efthymios Motohashi, Hozumi Mummery, Christine L Murata, Mitsuyoshi Nagao-Sato, Sayaka Nakachi, Yutaka Nakahara, Fumio Nakamura, Toshiyuki Nakamura, Yukio Nakazato, Kenichi van Nimwegen, Erik Ninomiya, Noriko Nishiyori, Hiromi Noma, Shohei Nozaki, Tadasuke Ogishima, Soichi Ohkura, Naganari Ohmiya, Hiroko Ohno, Hiroshi Onshima, Mitsuhiro Okada-Hatakeyama, Mariko Okazaki, Yasushi Orlando, Valerie Ovchinnikov, Dmitry A Pain, Arnab Passier, Robert Patrikakis, Margaret Persson, Helena Piazza, Silvano Prendergast, James G D Rackham, Owen J L Ramilowski, Jordan A Rashid, Mamoon Ravasi, Timothy Rizzu, Patrizia Roncador, Marco Roy, Sugata Rye, Morten B Saijyo, Eri Sajantila, Antti Saka, Akiko Sakaguchi, Shimon Sakai, Mizuho Sato, Hiroki Satoh, Hironori Savvi, Suzana Saxena, Alka Schneider, Claudio Schultes, Erik A Schultz-Tanzil, Gudula G Schwegmann, Anita Sengstag, Thierry Sheng, Guojun Shimoji, Hisashi Shimoni, Yishai Shin, Jay W Simon, Christophe Sugiyama, Daisuke Sugiyama, Takaaki Suzuki, Masanori Suzuki, Naoko Swoboda, Rolf K 't Hoen, Peter A C Tagami, Michihira Takahashi, Naoko Takai, Jun Tanaka, Hiroshi Tatsukawa, Hideki Tatum, Zuotian Thompson, Mark Toyoda, Hiroo Toyodo, Tetsuro Valen, Eivind van de Wetering, Marc van den Berg, Linda M Verardo, Roberto Vijayan, Dipti Vorontsov, Ilya E Wasserman, Wyeth W Watanabe, Shoko Wells, Christine A Winteringham, Louise N Wolvetang, Ernst Wood, Emily J Yamaguchi, Yoko Yamamoto, Masayuki Yoneda, Misako Yonekura, Yohei Yoshida, Shigehiro Zabierowski, Susan E Zhang, Peter G Zhao, Xiaobei Zucchelli, Silvia Summers, Kim M Suzuki, Harukazu Daub, Carsten O Kawai, Jun Heutink, Peter Hide, Winston Freeman, Tom C Lenhard, Boris Bajic, Vladimir B Taylor, Martin S Makeev, Vsevolod J Sandelin, Allbin Hume, David A Carninci, Piero Hayashizaki, Yoshihide Nature <London> Nature <London> Nature Publ. Group London [u.a.] 1476-4687 10.1038/nature12787 English 455 - 461 7493 507 Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation. PUB:(DE-HGF)16, ; 0, ; Atlases as Topic Cell Line Cells, Cultured Cluster Analysis Enhancer Elements, Genetic: genetics Gene Expression Regulation: genetics Genetic Predisposition to Disease: genetics HeLa Cells Humans Molecular Sequence Annotation Organ Specificity Polymorphism, Single Nucleotide: genetics Promoter Regions, Genetic: genetics RNA, Messenger: biosynthesis RNA, Messenger: genetics Transcription Initiation Site Transcription Initiation, Genetic RNA, Messenger Journal Article 2014 DZNE-2021-00605 2014 pmc:PMC5215096 pmid:24670763 https://pub.dzne.de/record/155338 https://doi.org/10.1038/nature12787