Pleiotropic Enhancers are Ubiquitous Regulatory Elements in the Human Genome

Abstract

Enhancers are regulatory elements of genomes that determine spatio-temporal patterns of gene expression. The human genome contains a vast number of enhancers, which largely outnumber protein-coding genes. Historically, enhancers have been regarded as highly tissue-specific. However, recent evidence has demonstrated that many enhancers are pleiotropic, with activity in multiple developmental contexts. Yet, the extent and impact of pleiotropy remain largely unexplored. In this study we analyzed active enhancers across human organs based on the analysis of both eRNA transcription (FANTOM5 consortium data sets) and chromatin architecture (ENCODE consortium data sets). We show that pleiotropic enhancers are pervasive in the human genome and that most enhancers active in a particular organ are also active in other organs. In addition, our analysis suggests that the proportion of context-specific enhancers of a given organ is explained, at least in part, by the proportion of context-specific genes in that same organ. The notion that such a high proportion of human enhancers can be pleiotropic suggests that small regions of regulatory DNA contain abundant regulatory information and that these regions evolve under important evolutionary constraints.

Keywords: CRE; enhancer; gene regulation; human genome; non-coding DNA; pleiotropy.

Fig. 1.

A large proportion of predicted human enhancers are pleiotropic. Proportion of pleiotropic enhancers as a function of the number of contexts considered in FANTOM5 (cyan) and ENCODE (magenta) enhancer sets. Boxplots indicate the median (horizontal line), interquartile range (box), observations within  ± 1.5xinterquartile range (whiskers) and outliers (dots). The proportion of pleiotropic enhancers when considering all organs in a single comparison are marked with a magenta line (ENCODE) and a cyan line (FANTOM5).

Fig. 2.

The majority of active enhancers in a particular organ are pleiotropic. Proportion of context-specific enhancers (green), pleiotropic enhancers active in two organs (orange) and pleiotropic enhancers active in more than two organs (blue) in FANTOM5 (A) and ENCODE (B) organs. The number of predicted enhancers per organ is indicated beside the name of each organ.

Fig. 3.

The proportion of context-specific enhancers is positively correlated with the proportion of context-specific genes. (A) Relationship between the proportion of context-specific enhancers and context-specific TSSs for the FANTOM5 data set. Active TSSs were defined in each organ by comparing their transcription levels against genomic background (see Materials and Methods for details). (B) Relationship between the proportion of context-specific enhancers and context-specific genes for the ENCODE dataset. An expression threshold was used to define expressed genes in each organ (see Materials and Methods for details).

Fig. 4.

Pleiotropic enhancers are enriched in SNPs with high regulatory potential. (A) The degree of pleiotropy of ENCODE enhancers is positively correlated with the enrichment in SNPs with high regulatory potential (Category 1 SNPs of Regulome DB). Black circles represent the odds ratio and bars represent the 95% CI. Enrichments (odds ratios) were calculated using common SNPs as background (see Materials and Methods for details). (B) The number of organs in which ENCODE enhancer SNPs are associated with changes in gene expression is positively correlated with the degree of pleiotropy of enhancers. Open circles indicate the mean number of organs in which a single SNPs is associated with changes in the expression of the same gene. Black circles represent the mean number of organs in which enhancers SNPs are associated with changes in the expression of any gene [considers cases in which (i) a single SNP regulates different genes in different organs, (ii) the same gene is regulated by different SNPs of the same enhancer in different organs, or (iii) when different SNPs of the same enhancer regulate different genes in different organs]. Bars represent the 95% CI.