Abstract
Super-enhancers (SEs) are critical for the transcriptional regulation of gene expression. We developed the super-enhancer archive version 3.0 (SEA v. 3.0, http://sea.edbc.org) to extend SE research. SEA v. 3.0 provides the most comprehensive archive to date, consisting of 164 545 super-enhancers. Of these, 80 549 are newly identified from 266 cell types/tissues/diseases using an optimized computational strategy, and 52 have been experimentally confirmed with manually curated references. We now support super-enhancers in 11 species including 7 new species (zebrafish, chicken, chimp, rhesus, sheep, Xenopus tropicalis and stickleback). To facilitate super-enhancer functional analysis, we added several new regulatory datasets including 3 361 785 typical enhancers, chromatin interactions, SNPs, transcription factor binding sites and SpCas9 target sites. We also updated or developed new criteria query, genome visualization and analysis tools for the archive. This includes a tool based on Shannon Entropy to evaluate SE cell type specificity, a new genome browser that enables the visualization of SE spatial interactions based on Hi-C data, and an enhanced enrichment analysis interface that provides online enrichment analyses of SE related genes. SEA v. 3.0 provides a comprehensive database of all available SE information across multiple species, and will facilitate super-enhancer research, especially as related to development and disease.
Highlights
Super-enhancers (SEs) are enhancer clusters bound by master transcription factors
In 2015, we proposed and built a database named the Super Enhancer Archive (SEA v. 1.0 http://sea.edbc.org), with the aim to provide a comprehensive archive of super-enhancers in numerous species [15]. dbSUPER provides a SE list from the mouse and human genome [16]
H3K27ac, BRD4, Med1 and p300 datasets by ChIP-Seq of 266 cell types/tissues/diseases for 11 species were collected from the public ENCODE, Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) databases
Summary
Super-enhancers (SEs) are enhancer clusters bound by master transcription factors. SEs affect the transcriptional activation of most genes, and participate in disease development, cell differentiation and tissue type identity specification. H3K27ac modification, BRD4, Med1 and p300 associations, are all enriched in SEs compared with typical enhancers, as shown by ChIP-Seq data.
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