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Determinants of enhancer and promoter activities of regulatory elements

Nature Reviews Genetics volume 21, pages 71–87 (2020)Cite this article

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Abstract

The proper activities of enhancers and gene promoters are essential for coordinated transcription within a cell. Although diverse methodologies have been developed to identify enhancers and promoters, most have tacitly assumed that these elements are distinct. However, studies have unexpectedly shown that regulatory elements may have both enhancer and promoter functions. Here we review these results, focusing on the factors that determine the promoter and/or enhancer activity of regulatory elements. We discuss emerging models that define regulatory elements by accessible DNA and their non-mutually-exclusive abilities to drive transcription initiation (promoter activity) and/or to enhance transcription at other such regions (enhancer activity).

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Fig. 1: Features used to distinguish promoters and enhancers.
Fig. 2: Chromatin features used to identify and distinguish enhancers and promoters are correlated with the promoter activity of regions, regardless of genomic location.
Fig. 3: General model of regulatory elements and of features associated with promoter and enhancer potential.
Fig. 4: A TF and RNAPII-centric cooperative model of transcriptional regulation.

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Acknowledgements

R.A. was supported by the Independent Research Fund Denmark (6108-00038B), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (StG no. 638173), and the Novo Nordisk Foundation (NNF18OC0052570). A.S. was supported by the ERC under the European Union’s Horizon 2020 research and innovation programme (MSCA ITN pHioniC), the Lundbeck Foundation, the Danish Cancer Society, the Danish Council for Independent Research and Innovation Fund Denmark. We thank L. van Duin, M. Wu and A. Thieffry for critical comments on the manuscript.

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  1. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Robin Andersson & Albin Sandelin

  2. Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark

    Albin Sandelin

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Glossary

RNA polymerase II

(RNAPII). An enzyme that catalyses the transcription of DNA to RNA, including mRNAs and many long non-coding RNAs.

Transcription start site

(TSS). The first transcribed genomic nucleotide of a transcript.

General transcription factors

(GTFs). Proteins that, together with RNA polymerase II, make up the pre-initiation complex.

Pre-initiation complex

A polypeptide complex consisting of RNA polymerase II and general transcription factors. This forms around the transcription start site and primes RNA polymerase II for transcription.

TATA box

A T/A-rich sequence that lies upstream (typically 24–30 bp) of transcription start sites, with a role in positioning the pre-initiation complex.

INR

The initiator sequence; a sequence pattern often overlapping transcription start sites.

Transcription factors

(TFs). Sequence-specific DNA-binding proteins with a role in regulating transcription.

Nucleosome-depleted region

(NDR). A region depleted of nucleosomes, often identified by DNaseI hypersensitivity, and often carrying regulatory potential.

Nascent-RNA techniques

A wide range of methods aimed at capturing RNA as it is being transcribed. See Box 2.

DNase-seq

A method for identifying accessible regions of the genome, based on DNaseI hypersensitivity. See Box 3.

Promoter-upstream transcript

(PROMPT). A short RNA (also known as upstream antisense RNA (uaRNA)) that is transcribed upstream and on the opposite strand from an mRNA transcription start site and is typically degraded by the nuclear exosome. It has many similarities to an enhancer RNA.

Nuclear exosome

A multi-protein complex responsible for the degradation of RNAs from the 3′ end.

Poly(A) sites

Sequence patterns (AT/ATAA) associated with the 3′ ends of genes, but that also occur with high frequency in intergenic DNA.

ChIP–seq

Chromatin immunoprecipitation coupled to sequencing; a method for finding DNA–protein interactions by combining immunoprecipitation and high-throughput DNA sequencing. See Box 3.

Enhancer RNAs

(eRNAs). Short RNAs (<500 bp) that are transcribed from enhancers, with many similarities to promoter-upstream transcripts (PROMPTs).

ATAC-seq

Assay for transposase-accessible chromatin; a method for identifying accessible regions of the genome, based on transposase activity.

CpG islands

Genomic sequences that are not depleted of cytosine–phosphate–guanine (CpG) dinucleotides, which would occur by 5-methylcytosine deamination. They often overlap or are near transcription start sites. Most definitions set a minimum length (for example, 200 or 500 bp) and a minimum observed/expected CpG ratio.

CAGE

Cap analysis of gene expression; a method to identify transcription start sites by sequencing the 5′ ends of capped, steady-state RNAs. See Box 2.

Expression quantitative trait loci

(eQTLs). Regions of DNA in which genetic variation is associated with variability in the expression of one or more genes.

Massively parallel reporter assays

(MPRAs). Methods that can measure the promoter or enhancer activity of many candidate DNA sequences in parallel. See Box 5.

DNase hypersensitive sites

(DHSs). Highly accessible genomic regions identified by DNase-seq.

Pioneer transcription factors

Transcription factors that can directly bind nucleosomal DNA, possibly in compacted chromatin.

Homotypic attraction

A force driving chromatin with similar characteristics or associated proteins to self-associate. The physical association may be formed by protein bridges or liquid–liquid phase separation, the latter of which involves molecules separating into liquid condensates with specific compositions.

Ascertainment bias

Drawing general conclusions based on biased sampling of non-representative examples.

Validation creep

Treating predictions as validated entities, in either the same study or subsequent studies. This type of bias is related to ascertainment bias and overfitting.

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Andersson, R., Sandelin, A. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet 21, 71–87 (2020). https://doi.org/10.1038/s41576-019-0173-8

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