Journal Article

Transcriptional enhancers: from properties to genome-wide predictions

Stampfel, Gerald, Shlyueva, Daria, Stark, Alexander

2014

Overview

Key Points The development of all organisms relies on differential gene expression, which is controlled by genomic regions called enhancers or cis -regulatory modules (CRMs). Recent studies highlight the importance of enhancers in evolution and disease; however, our understanding of their properties and functions remains incomplete. Enhancers contain short DNA sequences, which are binding sites for transcription factors. In turn, transcription factors recruit cofactors, which modify the nearby chromatin and lead to transcriptional activation. The location of putative enhancers can be predicted genome wide by assessing either the binding of transcription factors and cofactors or post-translational histone modifications by chromatin immunoprecipitation followed by deep sequencing (ChIP–seq). 'Open' chromatin with accessible DNA can be detected by DNase I hypersensitive site sequencing (DNase-seq), micrococcal nuclease sequencing (MNase-seq), formaldehyde-assisted isolation of regulatory elements followed by deep sequencing (FAIRE–seq) or assay for transposase-accessible chromatin using sequencing (ATAC-seq). Distal enhancers can activate target gene expression by looping to promoters. Such spatial contacts can be detected by chromosome conformation capture (3C) assays and its variants circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C) and Hi-C methods or by chromatin interaction analysis with paired-end tag sequencing (ChIA–PET, which is a combination of ChIP and various 3C-based methods). The genome-wide prediction of enhancers based on characteristic chromatin features is powerful, but such results have to be interpreted with caution because none of the known features is perfectly predictive. Enhancer activities of candidate sequences can be measured directly in a developmental context using image-based readouts or enhancer-FACS-seq. High-throughput parallel enhancer assays use either ectopic reporters to test thousands of candidates (which are based on DNA barcodes) or genome-wide screens (such as self-transcribing active regulatory region sequencing (STARR-seq)). Our understanding of enhancer biology will be further accelerated by advances in genome editing methods (such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat (CRISPR)–Cas9 system), as well as by the development or improvements of methods to assess gene expression, chromatin state and structure in entire genomes and from increasingly few cells (such as thousands of reporters integrated in parallel (TRIP), single-cell RNA sequencing or ChIP–seq, and high-resolution Hi-C). Enhancers are DNA elements that are key regulators of gene expression, but their complexities and context dependence makes their identification and characterization challenging. This Review discusses how an improved understanding of the varied properties of enhancers is being used in diverse approaches for the systematic prediction of enhancers genome wide. Cellular development, morphology and function are governed by precise patterns of gene expression. These are established by the coordinated action of genomic regulatory elements known as enhancers or cis -regulatory modules. More than 30 years after the initial discovery of enhancers, many of their properties have been elucidated; however, despite major efforts, we only have an incomplete picture of enhancers in animal genomes. In this Review, we discuss how properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies. We also cover recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity. Finally, we discuss recent technological advances and current challenges in the field of regulatory genomics.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/208/200 / 631/208/726/2102 / 631/337/100 / 631/553/2711 / Agriculture / Animal development / Animal Genetics and Genomics / Animals / Binding Sites / Biomedicine / Cancer Research / Chromatin - genetics / Chromatin - metabolism / Embryos / Enhancer Elements, Genetic - physiology / Epigenesis, Genetic / Gene expression / Gene Function / Genetic aspects / Genetic research / Genetic transcription / Genome / Genome-Wide Association Study / Genomes / Genomics / Human Genetics / Humans / review-article / RNA polymerase / Transcription factors / Transcription Factors - metabolism / Transcription, Genetic