An atlas of active enhancers across human cell types and tissues
By R. Andersson, C. Gebhard, Irene Miguel-Escalada, I. Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki and 40 more. Nature, 2014
2,469 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/388866e41050077cad13e04a9af8dacd73aff6d4
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Wyeth W. Wasserman
- David Haussler
- Wenqiang Shi
- Albin Sandelin
- Boris Lenhard
- Yifeng Li
- Robert M. Kuhn
- Melissa A. Haendel
Citations in the corpus
- BRD4 and Cancer: going beyond transcriptional regulation (2018, background): “Many active ENHs have been shown to be site of active transcription for short (less than 200 nt) and bidirectional RNAs, which in turn assist ENHs in promoting target genes expression [40, 41].”
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “Thus, eRNAs have been shown to be significantly co-expressed with the promoters that they regulate (22, 29).”
- Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters (2015, positive): “Based on the FANTOM5 promoter and enhancer atlases [23,2], each sample comes from one of the three classes of annotated DNA regions including active enhancer regions, active promoter regions, and background.”
- EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species (2019, methodology): “jp/5/datafiles/latest/extra/Enhancers/) (2).”
- DEEP: a general computational framework for predicting enhancers (2014, methodology): “We used ‘genuine‘ enhancers recently published by the FANTOM5 consortium (27).”