What's EP-Atlas?

Identifying enhancer–promoter connectivity remains a major challenge in modern biology. Distinct from conventional DNA proximity–based approaches, we recently demonstrated that such connectivity can be accurately inferred through pairwise interactions between enhancer RNAs (eRNAs) and promoter upstream antisense RNAs (uaRNAs, also known as PROMPTs). To support systematic exploration of this RNA-mediated regulatory layer, we developed EP-Atlas, a curated database dedicated to cataloging enhancer–promoter RNA interactions (EPRIs).

To achieve global mapping of EPRIs, we integrated high-throughput RNA conformation capture techniques—including RIC-seq, PARIS, and KARR-seq—to identify chimeric reads reflecting in vivo eRNA–uaRNA proximity. These RNA interaction data were intersected with enhancer and promoter regions defined by ChIP-seq, enabling systematic identification of direct eRNA–uaRNA interactions across the genome. EP-Atlas currently encompasses 360,261 high-confidence interaction pairs derived from ten human cell lines—HeLa, HepG2, hNPC, HEK293T, GM12878, K562, HT29, A549, IMR90, and H1 hESC—providing a comprehensive resource for studying RNA-mediated enhancer–promoter connectivity.

Search Box

Search by gene

Gene symbol

Function introduction:
Users can submit either a gene symbol or an Ensembl ID (ENSG) to explore potential enhancer–promoter interactions associated with that gene across different cell types. These interactions, identified under various computational strategies, may indicate regulatory mechanisms that influence gene expression.

Basic information:
1) Species: Human.
2) Gene symbol: Users submit a gene symbol or an Ensembl Gene ID.
3) All coordinates are based on the human reference genome GRCh37 (also known as hg19).

Search by enhancer name

Cell line

Enhancer type

Enhancer number

Function introduction:
By submitting an enhancer ID, users can identify associated promoter interactions and downstream genes potentially regulated by the enhancer. These interactions provide insights into the gene regulatory networks mediated by enhancer–promoter connections.

Basic information:
1) Cell line: 10 different human cell lines.
2) Enhancer type: typical enhancer (TE) and super enhancer (SE).
3) Enhancer number: enhancer ID in each cell line.

Search by enhancer region

Position

Function introduction:
Users can submit the genomic coordinates of an enhancer to compare it with entries in the database. The system will identify enhancers that either overlap with the submitted region or fall within a ±10 kb window upstream or downstream, allowing users to explore detailed information about the matched enhancers.

Basic information:
1) Enhancer start: Enhancer start region (please enter an integer).
2) Enhancer end: A larger integer less than the length of relative chromosome.