Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

Abstract

Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ∼42% of zebrafish SEs were located in close proximity to orthologs that also were associated with SEs in mouse and human. Compared to their nonassociated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish annotations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

“…https://doi.org/10.1371/journal.pgen.1008546.g001 putative enhancers increases during the stages prior to gene activation. Here, we used zebrafish enhancers from adult tissues as a control [35]. At these enhancers, chromatin accessibility did not increase from 256-cell to 80% epiboly, confirming that the changes in accessibility at enhancers are not due to a general increase in accessibility.…”

“…We summed the expression level of genes reported in [16] until 8hpf and defined a cut-off of RPKM < 0.1 to select genes not expressed until shield stage as a control group. For enhancers we used late-activated enhancers [35] as a control.…”

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

“…As for promoters, accessibility of putative enhancers increases during the stages prior to gene activation. Here, we used zebrafish enhancers from adult tissues as a control [34]. At these enhancers, chromatin accessibility did not increase from 256-cell to 80% epiboly, confirming that the changes in accessibility at enhancers are not due to a general increase in accessibility.…”

“…We summed the expression level of genes reported in [16] 19 until 8hpf and defined a cut-off of RPKM < 0.1 to select genes not expressed until shield stage as a control group. For enhancers we used late-activated enhancers [34] Promoters Enhancers Figure 3. Chromatin accessibility at regulatory elements increases prior to gene activity.…”

High-resolution comparative analysis of great ape genomes

“…3c-e). Interestingly, 139 of the fhSVs intersect with regions recently classified as super-enhancers (34). A comparison with a previous analysis of human-conserved deletions (hCONDELs) from earlier versions of the human, chimpanzee and macaque genomes (5) confirms that 77% (451/583) of the hCONDELs intersect the fhDELs, with the remainder corresponding primarily to polymorphic events in the human population (Fig.…”