Vanja Haberle, Cosmas D. Arnold, Michaela Pagani, Martina Rath, Katharina Schernhuber et al.
Transcriptional cofactors (COFs) communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression. Although some COFs have been shown to prefer certain promoter types over others (e.g. refs. 6,7), the extent to which different COFs display intrinsic specificities for distinct promoters is unclear. Here, we use a high-throughput promoter-activity assay in Drosophila melanogaster S2 cells to screen 23 COFs for their ability to activate 72,000 candidate core promoters (CPs). We observe differential activation of CPs, indicating distinct regulatory preferences or compatibilities between COFs and specific types of CPs. These functionally distinct CP types are differentially enriched for known sequence elements, such as the TATA-box, Downstream Promoter Element (DPE), or TCT motif and display distinct chromatin properties at endogenous loci. Importantly, the CP types differ in their relative abundance of H3K4me3 and H3K4me1, suggesting that these histone modifications might distinguish trans regulatory factors rather than promoter- versus enhancer-type cis elements. We confirm the existence of distinct COF-CP compatibilities in two additional Drosophila cell lines and in human cells, for which we find COFs that prefer TATA-box or CpG island promoters, respectively. Distinct compatibilities between COFs and promoters can explain how different enhancers specifically activate distinct sets of genes, alternative promoters within the same genes, and distinct transcription start sites within the same promoters. Thus, cofactor-promoter compatibilities may underlie distinct transcriptional programs in species as divergent as flies and human.
Vanja Haberle, Cosmas D. Arnold, Michaela Pagani, Martina Rath, Katharina Schernhuber, Alexander Stark. Transcriptional cofactors display specificity for distinct types of core promoters. 2019-05-15. https://doi.org/10.1038/s41586-019-1210-7
The shared 72,000-element Drosophila core-promoter library was assayed in Drosophila Kc167 cells with GAL4-DBD recruitment of six cofactors, P65, and GFP. Each condition was measured in three biological replicates by UMI-collapsed STAP-seq.
The shared 72,000-element Drosophila core-promoter library was assayed in Drosophila ovarian somatic cells (OSC) with GAL4-DBD recruitment of six cofactors, P65, and GFP. Each condition was measured in three biological replicates by UMI-collapsed STAP-seq.
A 12,000-element representative human promoter/enhancer/control oligonucleotide library was assayed in HCT116 cells with GAL4-DBD recruitment of five human cofactors, P65, and GFP. Each condition was measured in three biological replicates by UMI-collapsed STAP-seq.
A 72,000-element Drosophila core-promoter oligonucleotide library was assayed in S2 cells while individual GAL4-DBD-tethered cofactors were recruited to a 4xUAS reporter. Three biological replicates were generated for 23 cofactors plus P65 and GFP controls, and productive reporter initiation was quantified by UMI-collapsed STAP-seq tags.
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