A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

Abstract

Millions of cis-regulatory elements are predicted in the human genome, but direct evidence for their biological function is still scarce. Here we report a high-throughput method, Cis-Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome. We use it to interrogate the 2Mbp POU5F1 locus in the human embryonic stem cells and identify 45 cis-regulatory elements of POU5F1. A majority of these elements display active chromatin marks, DNase hypersensitivity and occupancy by multiple transcription factors, confirming the utility of chromatin signatures in cis elements mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. Taken together, these results support the utility of CREST-seq for large-scale cis regulatory element discovery and point to commonality of enhancer-like promoters in the human genome.

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

“…Interestingly, the percentage increased to 58.4% when testing elements overlapping housekeeping promoters (Arnold et al 2013;Zabidi et al 2015), indicating that these regions have different inherent properties. Moreover, the deletion of a number of promoter regions in mammals altered the transcription of distal genes in cis, in keeping with an enhancer-like function (Dao et al 2017;Diao et al 2017). While indirect effects of the deletions on chromatin topology or other mechanisms cannot be excluded in these studies, the accumulating evidence suggests that some promoters have enhancer activity.…”

“…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).…”

Variant Interpretation: Functional Assays to the Rescue

“…Cas9 can also be used to delete larger regions, leading to a better understanding of the effects of copy-number variation. 78,79 However, breakpoints will have to be carefully chosen given that an effectively infinite number of copy-number variants are possible.…”

High-Throughput Approaches to Pinpoint Function within the Noncoding Genome

“…Targeting the coding sequence of the gene of interest can serve as a positive control in noncoding screens (Canver et al, 2015, 2017a; Sanjana et al, 2016). Alternatively, targeting GFP can serve as a positive control in pooled screen experiments using a GFP reporter-based readout (Diao et al, 2017; Rajagopal et al, 2016), and targeting universally essential genes, such as ribosomal genes, can serve as a positive control for dropout screens (Shalem et al, 2014; Wang et al, 2014). …”