Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium (March 2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836
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.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | *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/genetics Transcription Initiation Site Transcription Initiation, Genetic |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Gene Regulation and Cell Proliferation CSHL labs > Gingeras lab |
| Depositing User: | Matt Covey |
| Date: | 27 March 2014 |
| Date Deposited: | 13 Oct 2015 18:59 |
| Last Modified: | 16 Jul 2021 16:02 |
| PMCID: | PMC5215096 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31919 |
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