Bernardo P. de Almeida, Franziska Reiter, Michaela Pagani, Alexander Stark
Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood, and de novo enhancer design has been challenging. Here, we built a deep-learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally nonequivalent instances of the same TF motif that are determined by motif-flanking sequence and intermotif distances. We validated these rules experimentally and demonstrated that they can be generalized to humans by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.
Bernardo P. de Almeida, Franziska Reiter, Michaela Pagani, Alexander Stark. DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. 2022-05-12. https://doi.org/10.1038/s41588-022-01048-5
A Twist-synthesized 249-bp oligo library containing wild-type Drosophila enhancers, motif mutants, flank-swap and scanning-mutagenesis constructs, Med14 shuffle-bin constructs, and de novo synthetic enhancers was tested in S2 cells with developmental and housekeeping core promoters. Three biological replicates were performed for each promoter screen.
A Twist-synthesized library of 249-bp human enhancer wild-type and motif-mutant sequences, together with negative genomic controls, was tested in HCT116 cells in two biological replicates. The processed table retains oligos with sufficient plasmid-input coverage and complete author-supplied log2 activity values.
A sheared genomic DNA library from Drosophila melanogaster strain y; cn bw sp was tested in S2 cells with DSCP developmental and Rps12 housekeeping core promoters in two biological replicates. The processed table contains merged developmental and housekeeping peak calls and their RNA/input enrichment measurements.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 8 files (ZIP)GSE183936_S2_dev_STARRseq_merged.peaks.txt.gzGSE183936_S2_hk_STARRseq_merged.peaks.txt.gzGSE183937_S2_oligo_library_counts.txt.gzGSE183938_HCT116_oligo_library_counts.txt.gzREADME.txtSTARRseq_data_DeepSTARR_predictions.txtTable_synthetic_enhancers.txtTwist_mutagenesis_Drosophila_final_table.txt