High-throughput functional comparison of promoter and enhancer activities

Abstract

Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We measured the enhancer and promoter activities of thousands of DNA fragments transduced into mouse neurons. We focused on genomic loci bound by the neuronal activity-regulated coactivator CREBBP, and we measured enhancer and promoter activities both before and after neuronal activation. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, whereas others are not. Although the specific biases we observe may be dependent on experimental or cellular context, our results suggest that gene promoters are distinguished from distal enhancers by specific complements of transcriptional activators.

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

“…Recent high-throughput studies indicate that the same sequences can function as both promoters and enhancers in vitro, although gene promoters generated more promoter activity compared with distal elements (Nguyen et al 2016;van Arensbergen et al 2017). While our results also show that the same sequences can harbor both activities, we uncovered some key differences.…”

“…This suggests a relationship between the level of eRNA and an enhancer's inherent capacity to act as a promoter in vivo, although we note that the number of tested enhancers is low. In all four cases, the relative intensity of promoter signal was much weaker than that of the enhancer-driven expression, a feature also observed in mammalian cells (Nguyen et al 2016;van Arensbergen et al 2017). …”

“…A number of recent studies using large-scale cell culture assays indicate that a fraction of promoters can act as enhancers (Arnold et al 2013;Zabidi et al 2015;Nguyen et al 2016;Dao et al 2017;Diao et al 2017). Here, we investigated whether this also holds true in a chromatinized background during embryonic development.…”

“…The majority of studies investigating common functional properties between promoters and enhancers (Nguyen et al 2016;Dao et al 2017;Diao et al 2017;van Arensbergen et al 2017) has used cell culture-based approaches, relying on transient transfection that can be performed at a large scale. However, these assays function outside of a normal chromatinized context, an important property known to affect both promoter (transcriptional initiation) (Archer et al 1992) and enhancer (Inoue et al 2017) activity through various mechanisms (Jeong and Stein 1994;Hebbar and Archer 2008).…”

“…A number of studies have measured the ability of different genomic elements to function as either enhancers or promoters using massively parallel cell culture-based reporter assays. Measuring promoter activity of thousands of small DNA elements (Nguyen et al 2016) or across the entire human genome (van Arensbergen et al 2017) suggests that many enhancers (as well as repetitive elements) can act as weak autonomous promoters, although at levels ∼10-fold lower than that of annotated gene promoters. Conversely, testing promoters for enhancer activity revealed that ∼3% of human elements (Dao et al 2017) and 4.5% of Drosophila elements (Arnold et al 2013) spanning promoters have in vitro enhancer activity.…”