Miguel Martinez-Ara, Federico Comoglio, Joris van Arensbergen, Bas van Steensel
Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterized in mammalian cells. We used high-throughput combinatorial reporter assays to test thousands of CRE-promoter pairs from three Mb-sized genomic regions in mouse cells. This revealed that CREs vary substantially in their promoter compatibility, ranging from striking specificity to broad promiscuity. More than half of the tested CREs exhibit significant promoter selectivity. Housekeeping promoters tend to have similar CRE preferences, but other promoters exhibit a wide diversity of compatibilities. Higher-order transcription factors (TF) motif combinations may account for compatibility. CRE-promoter selectivity does not correlate with looping interactions in the native genomic context, suggesting that chromatin folding and compatibility are two orthogonal mechanisms that confer specificity to gene regulation.
Miguel Martinez-Ara, Federico Comoglio, Joris van Arensbergen, Bas van Steensel. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome. 2022-07-07. https://doi.org/10.1016/j.molcel.2022.04.009
An episomal Upstream combinatorial MPRA library tested pairwise combinations of approximately 450-bp DNase-hypersensitive candidate CREs and GENCODE-annotated promoter fragments from the Klf2 genomic locus. The clean table preserves both cloned orientations and reports normalized reporter activity and corrected cCRE-promoter boost indices across three biological replicates in E14TG2a mouse embryonic stem cells.
An episomal Downstream combinatorial MPRA library tested Klf2-locus cCREs downstream of reporter constructs carrying one of ten selected promoters. The clean table preserves both cCRE orientations and reports normalized reporter activity, the deposited adjusted boost statistic, and corrected cCRE-promoter boost indices across three biological replicates in E14TG2a mouse embryonic stem cells.
An episomal Upstream combinatorial MPRA library tested pairwise combinations of approximately 450-bp DNase-hypersensitive candidate CREs and GENCODE-annotated promoter fragments from the Tfcp2l1 genomic locus. The clean table preserves both cloned orientations and reports normalized reporter activity and corrected cCRE-promoter boost indices across three biological replicates in E14TG2a mouse embryonic stem cells.
An episomal Upstream combinatorial MPRA library tested pairwise combinations of approximately 450-bp DNase-hypersensitive candidate CREs and GENCODE-annotated promoter fragments from the Nanog genomic locus. The clean table preserves both cloned orientations and reports normalized reporter activity and corrected cCRE-promoter boost indices across three biological replicates in E14TG2a mouse embryonic stem cells.
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 10 files (ZIP)GSE186265_Activities_allcombinations_Upstream.tsv.gzGSE186265_ActivitiesAndBoostIndices_Downstream.tsv.gzGSE186265_BoostIndices_cCRE-P_Upstream.tsv.gzmmc1.pdfmmc2.xlsxmmc3.xlsxmmc4.xlsxmmc5.xlsxmmc6.pdfREADME.txt