An atlas of active enhancers across human cell types and tissues

Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner, Eivind Valen, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin, Frederik Otzen BaggerMette Jørgensen, Peter Refsing Andersen, Nicolas Bertin, Owen Rackham, A Maxwell Burroughs, J Kenneth Baillie, Yuri Ishizu, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Yutaka Negishi, Christopher J Mungall, Terrence F Meehan, Timo Lassmann, Masayoshi Itoh, Hideya Kawaji, Naoto Kondo, Jun Kawai, Andreas Lennartsson, Carsten O Daub, Peter Heutink, David A Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, FANTOM Consortium, Robert S Young (Member of Consortium), Malcolm E Fisher (Member of Consortium), Alison Meynert (Member of Consortium), James G D Prendergast (Member of Consortium), Martin S Taylor (Member of Consortium)

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.
Original languageEnglish
Pages (from-to)455-61
Number of pages7
Issue number7493
Publication statusPublished - 26 Mar 2014


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