An atlas of active enhancers across human cell types and tissues

R Andersson; C Gebhard; I Miguel-Escalada; I Hoof; J Bornholdt; M Boyd; Y Chen; X Zhao; C Schmidl; T Suzuki; E Ntini; E Arner; E Valen; K Li; L Schwarzfischer; D Glatz; J Raithel; B Lilje; N Rapin; FO Bagger; M Jørgensen; PR Andersen; N Bertin; O Rackham; AM Burroughs; JK Baillie; Y Ishizu; Y Shimizu; E Furuhata; S Maeda; Y Negishi; CJ Mungall; TF Meehan; T Lassmann; M Itoh; H Kawaji; N Kondo; J Kawai; A Lennartsson; CO Daub; P Heutink; DA Hume; TH Jensen; H Suzuki; Y Hayashizaki; F Müller; ARR Forrest; P Carninci; M Rehli; A Sandelin

Journal article

An atlas of active enhancers across human cell types and tissues

R Andersson, C Gebhard, I Miguel-Escalada, I Hoof, J Bornholdt, M Boyd, Y Chen, X Zhao, C Schmidl, T Suzuki, E Ntini, E Arner, E Valen, K Li, L Schwarzfischer, D Glatz, J Raithel, B Lilje, N Rapin, FO Bagger Show all

Nature | NATURE PORTFOLIO | Published : 2014

DOI: 10.1038/nature12787

Abstract

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 differ..

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University of Melbourne Researchers

Christine Wells Author

Grants

Awarded by Novo Nordisk

Funding Acknowledgements

FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y.H. and a Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan, to Y.H. The A. S. group was supported by funds from the European Research Council FP7/2007-2013/ERC no. 204135, the Novo Nordisk and Lundbeck foundations. Work in the M. R. group was funded by grants from the Deutsche Forschungsgemeinschaft (RE1310/7,11,13) and Rudolf Bartling Stiftung. F. M. and I. M. E. were supported by "BOLD" MarieCurie ITN and "ZF-Health" Integrated project of the European Commission. We thank S. Noma, M. Sakai and H. Tarui for RNA-seq and sRNA-seq preparation, RIKEN GeNAS for generation and sequencing of the Heliscope CAGE libraries, Illumina RNA-seq and sRNA-seq, the Copenhagen National High-throughput DNA Sequencing Center for Illumina CAGE-seq, M. Edinger, P. Hoffmann and R. Eder for cell sorting, A. Albrechtsen, I. Moltke, W. Wasserman for advice, and the Netherlands Brain Bank for post-mortem human brain material.