Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

• Published in: Nature communications Vol. 15; no. 1; pp. 8584 - 11
• Main Authors: Loubiere, Vincent, de Almeida, Bernardo P., Pagani, Michaela, Stark, Alexander
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03-10-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/47; 49; 631/337; 631/337/572/2102; Animals; Cell Line; Cooperativity; DNA-Binding Proteins; Drosophila melanogaster - genetics; Drosophila melanogaster - metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Enhancer Elements, Genetic; Enhancers; Fruit flies; Gene Expression Regulation, Developmental; Gene regulation; Genes; Genes, Essential; Genomics; Humanities and Social Sciences; Impact analysis; Insects; multidisciplinary; Promoter Regions, Genetic; Promoters; Science; Science (multidisciplinary); Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; Twist-Related Protein 1
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52921-2

Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target promoters. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these cooperate to regulate transcription. Using
Drosophila melanogaster
S2 cells as a model, we assay the activities of more than a thousand individual enhancers and about a million enhancer pairs toward housekeeping and developmental core promoters with STARR-seq. We report that housekeeping and developmental enhancers show distinct modes of enhancer-enhancer cooperativity: while housekeeping enhancers are additive such that their combined activity mirrors the sum of their individual activities, developmental enhancers are super-additive and combine multiplicatively. Super-additivity between developmental enhancers is promiscuous and neither depends on the enhancers’ endogenous genomic contexts nor on specific transcription factor motif signatures. However, it can be further boosted by Twist and Trl motifs and saturates for the highest levels of enhancer activity. These results have important implications for our understanding of gene regulation in complex multi-enhancer developmental loci and genomically clustered housekeeping genes, providing a rationale to interpret the transcriptional impact of non-coding mutations at different loci.
High-throughput analyses show that developmental enhancer pairs are super-additive, combining multiplicatively until saturation, while housekeeping enhancers are additive. Super-additivity is promiscuous, but boosted by Trl and Twist motifs.