PT  - JOURNAL ARTICLE
AU  - Porfirio Quintero-Cadena
AU  - Paul W. Sternberg
TI  - Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes
AID  - 10.1101/061218
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 061218
4099  - http://biorxiv.org/content/early/2016/06/28/061218.short
4100  - http://biorxiv.org/content/early/2016/06/28/061218.full
AB  - Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer-promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By re-analyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that non-specific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation.