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An atlas of active enhancers across human cell types and tissues

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 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.

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Figure 1: Bidirectional capped RNAs is a signature feature of active enhancers.
Figure 2: Features distinguishing enhancer TSSs from mRNA TSSs.
Figure 3: CAGE expression identifies cell-type-specific enhancer usage.
Figure 4: In vivo validation in zebrafish of tissue-specific enhancers.
Figure 5: Enhancer usage and specificity in groups of cells.
Figure 6: Linking enhancers to TSSs and disease-associated SNPs.

Accession codes

Primary accessions

DDBJ/GenBank/EMBL

Gene Expression Omnibus

Data deposits

The FANTOM5 atlas is accessible from http://fantom.gsc.riken.jp/5. FANTOM5 CAGE, RNA-seq and sRNA data have been deposited in DDBJ/EMBL/GenBank (accession codes DRA000991, DRA001101). Genome browser tracks for enhancers with user-definable expression specificity-constraints can be generated at http://enhancer.binf.ku.dk. Here, processed enhancer expression data, predefined enhancer tracks and motif finding results are also deposited. Blood-cell ChIP-seq data and CAGE data on exosome-depleted HeLa cells have been deposited in the NCBI GEO database (accession codes GSE40668, GSE49834).

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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 (RE 1310/7, 11, 13) and Rudolf Bartling Stiftung. F.M. and I.M.E. were supported by “BOLD” Marie Curie 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.

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R.A., I.H., E.A., E.V., K.L., Y.C., B.L., X.Z., M.J., H.K., T.F.M., T.L., N.B., O.R., A.M.B. , J.K.B, C.J.M, N.R., F.O.B., M.R., A.S. made the computational analysis. J.B., M.B., T.L., H.K., N.K., J.K., H.S., M.I., C.O.D, A.R.R.F., P.C., Y.H. prepared and pre-processed CAGE and/or RNA-seq libraries. E.N., P.R.A., T.H.J., J.B., M.B. made the knockdown experiments followed by CAGE. C.G., C.S., L.S., J.R., D.G., M.R. made the blood cell ChIP experiments, methylation assays and in vitro blood cell validations. T.S., C.G., Y.I., Y.S., E.F., S.M., Y.N., A.R.R.F., P.C. and H.S. made the HeLa/HepG2 in vitro validations. I.M.E., R.A., A.S., F.M. designed and carried out zebrafish in vivo tests. R.A., C.G., I.H., C.S., E.A., E.V., F.M., I.M.E., P.C., A.R.R.F, M.B., J.B., A.L., C.D., D.A.H., P.H., M.R., A.S. interpreted results. R.A., C.G., I.H., E.V., I.M.E., J.B., F.M., D.A.H., M.R., A.S. wrote the paper with input from all authors. M.R. and A.S. coordinated and supervised the project.

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Correspondence to Alistair R. R. Forrest, Piero Carninci, Michael Rehli or Albin Sandelin.

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This file contains Supplementary Text, Supplementary Table Legends, Supplementary References, a full list of members of the FANTOM consortium and Supplementary Figures 1-33. (PDF 19934 kb)

This file contains Supplementary Text, Supplementary Table Legends, Supplementary References, a full list of members of the FANTOM consortium and Supplementary Figures 1-33.

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Andersson, R., Gebhard, C., Miguel-Escalada, I. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014). https://doi.org/10.1038/nature12787

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