Lan T M Dao, Ariel O Galindo-Albarrán, Jaime A Castro-Mondragon, Charlotte Andrieu-Soler, Alejandra Medina-Rivera et al.
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters. Extensive CRISPR–Cas9 genomic manipulation demonstrated the involvement of these promoters in the cis regulation of expression of distal genes in their natural loci. Our results have important implications for the understanding of complex gene regulation in normal development and disease.
Lan T M Dao, Ariel O Galindo-Albarrán, Jaime A Castro-Mondragon, Charlotte Andrieu-Soler, Alejandra Medina-Rivera, Charbel Souaid, Guillaume Charbonnier, Aurélien Griffon, Laurent Vanhille, Tharshana Stephen, Jaafar Alomairi, David Martin, Magali Torres, Nicolas Fernandez, Eric Soler, Jacques van Helden, Denis Puthier, Salvatore Spicuglia. Genome-wide characterization of mammalian promoters with distal enhancer functions. 2017-06-05. https://doi.org/10.1038/ng.3884
Approximately 250-bp human promoter windows centered on annotated transcription start sites, together with positive and negative controls, were tested by CapStarr-seq in K562 cells. The table reports RNA/input fold-change and replicate activity calls for the two biological replicates.
A captured mouse DNase-I hypersensitive-region library was assayed with CapStarr-seq in the P5424 mouse lymphoma cell line. The table reports the source activity class for each assayed region.
Approximately 250-bp human promoter windows centered on annotated transcription start sites, together with positive and negative controls, were tested by CapStarr-seq in HeLa/HeLa-S3 cells. The table reports RNA/input fold-change and replicate activity calls for the two biological replicates.
A captured mouse DNase-I hypersensitive-region library was assayed with CapStarr-seq in NIH-3T3 fibroblasts. The table reports the source activity class for each assayed region.
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 11 files (ZIP)GSE60029_family.soft.gzGSE60029_RAW.tarGSE60029_series_matrix.txt.gzGSE83296_Capstarr_Human_data.txt.gzGSE83296_family.soft.gzGSE83296_RAW.tarSOURCES.txtsupp_table1_mouse_dhs_capstarr.xlsxsupp_table2_human_promoter_capstarr.xlsxsupp_table8_capstarr_sequencing_summary.xlsxsupplementary_text_figures.pdf