A body map of super-enhancers and their function in pig

Abstract

Introduction: Super-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs.

Methods: Here, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression.

Results: We observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression.

Discussion: In this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.

Keywords: features; function; pig; super-enhancers; tissue-specific.

Figure 1

The summary of super-enhancers in pig. (A) The overview of the current study design. (B) Super-enhancers (SEs) identified by ROSE based on H3K27ac signal in each tissue. Super-enhancers are colored based on tissue, and show exceptionally high signal. Tissue color is the same with (A). (C) The distribution of number, size, H3K27ac signal intensity and genome coverage of super-enhancers, and the number of enhancers, origin size of enhancers and gap between enhancers based on super-enhancers of 14 tissues.

Figure 2

The composition of super-enhancers in pig. (A) The percent of enhancer in normal-enhancers and super-enhancers. (B) The percent of each of five enhancer types in super-enhancers and normal enhancers. (C) The fold enrichment of super-enhancers in autosomes and X chromosome. (D) The fold enrichment of super-enhancers in four repeat sequences types.

Figure 3

The gene expression influenced by super-enhancers. (A) Genes with (11,514) and without (11,886) super-enhancers differed in the expression, tau, and conservation. The gene conservation score was sequence identity (%) from pig gene to orthologous human gene. (B) The effect of SE length on the gene expression, categorized into five groups (G1–G5) based on increasing SE size. (C) The expression of genes with different distances to SEs, classified into five groups (T1–T5) based on ascending distance values: two groups of downstream genes T1 (n = 4,225) and T2 (n = 1,982), one group of genes overlapping with SEs T3 (n = 1,000), and two groups of upstream genes T4 (n = 2,688) and T5 (n = 4,244).

Figure 4

Tissue-specific pattern of super-enhancers. (A) Clustering of 8,173 non-redundant super-enhancers based on their activity in each tissue. (B) GO function and representative genes in each super-enhancers cluster. (C) Motifs enriched in each super-enhancers cluster.

Figure 5

Super-enhancers in brain and liver tissues. (A) A brain-specific super-enhancer present at the CORO2B locus (chr1:166,239,933-167,241,533). (B) A liver-specific super-enhancer present at the PAH locus (chr5:81,236,096-81,453,790). Following sections are Hi-C, chromatin state, H3K4me1, H3K27ac, and RNA-seq. Vertical scale of UCSC tracks shows normalized signal from 0 to 100 for RNA-seq, 0 to 150 for H3K27ac, and 0 to 50 for H3K4me1. The red boxed areas are the range of SEs.