title: Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes.
abstract: 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 reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific 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.
authors: Division of Biology and Biological Engineering, California Institute of Technology, Howard Hughes Medical Institute, Pasadena, California 91125.
authors: Porfirio
authors: 0000-0003-0067-5844
authors: P
authors: Quintero-Cadena
authors: Division of Biology and Biological Engineering, California Institute of Technology, Howard Hughes Medical Institute, Pasadena, California 91125 pws@caltech.edu.
authors: Paul W
authors: PW
authors: Sternberg
mesh_terms: D000818:Animals; D004742:Enhancer Elements, Genetic; D056890:Eukaryota / Q000235:genetics*; D005786:Gene Expression Regulation; D023061:Gene Order; D005822:Genetic Vectors / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D011401:Promoter Regions, Genetic
keywords: enhancer sharing; enhancer specificity; gene coexpression; gene neighbors; transcriptional domains