Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

Variable allelic expression of imprinted genes at the Peg13, Trappc9, Ago2 cluster in single neural cells

“…To test these candidate elements in promoter-reporter gene assay, we first constructed a Luciferase plasmid that contained a 444 bp Trappc9 promoter fragment upstream of and including non-coding exon 1 ( Figure 1C ). The size of this promoter fragment is in line with standards from high-throughput testing of promoter-enhancer interactions in the mouse genome ( Martinez-Ara et al, 2022 ). We positioned the candidate regulatory elements downstream or upstream of the promoter-reporter gene cassette, depending on their relative locations within the Trappc9 locus ( Figures 6A,B ).…”

“…However, there is currently no widely accepted consensus for a silencer chromatin signature and many silencer elements might be bifunctional elements acting through various mechanisms ( Segert et al, 2021 ). Furthermore, a recent functional study of ENCODE3 candidate cis-regulatory elements (cCREs) found that the majority of annotated cCREs had no effect on transcription, while similar numbers of the remaining elements had enhancer or repressor activity, respectively, which was surprising given that cCREs are predicted to be enhancers ( Martinez-Ara et al, 2022 ). Further experiments will be required to determine whether the silencer elements we identified within the Trappc9 locus might function in an allele-specific way and contribute to the brain-specific imprinted expression bias of this gene.…”

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

“…Specifically, the Triml1/2 and Zfp42 promoters can be activated by embryonic Fat1 enhancers in their TAD, but only when relocated away from their endogenous positions. This is significant as the extent to which enhancer-promoter compatibility regulates mammalian transcription remains controversial and is largely examined outside of native contexts in episomal in vitro assays ( Bergman et al., 2021 ; Martinez-Ara et al., 2022 ; Ray-Jones and Spivakov, 2021 ; van Arensbergen et al., 2014 ). As result, such approaches may fail to predict many endogenous gene expression outcomes found in native regulatory landscapes ( Arnold et al., 2017 ; Martinez-Ara et al., 2022 ).…”

The logic of native enhancer-promoter compatibility and cell-type-specific gene expression variation

“…However, in other analyses, enhancers show remarkable specificity and activate some but not other promoters 9, 14–17 . In massively parallel reporter assays (MPRAs), a majority of Drosophila and mouse enhancers show promoter specificity 18, 19 , and the compatibility information appears to be sequence-encoded in the enhancers and promoters 18, 20 . Supporting E-P specificity, different groups of human enhancers use different cofactors (COFs) 21 , and different COFs activate different promoters in Drosophila 22 .…”

“…These findings present two seemingly diverging models of enhancer specificity. In one model, enhancers are broadly compatible with diverse promoters [11][12][13] , while in another model, E-P compatibility is restricted such that enhancers activate selected promoters with high specificity [14][15][16][17][18][19] . An attractive aspect of the sequence-encoded E-P compatibility model is that it can rationalize why enhancers frequently skip their nearest genes and connect with distal genes 4-10 , how specificity can be achieved in phase-separated enhancer condensate hubs [23][24][25] , and how enhancers differentially activate alternative promoters within the same genes 22 .…”