Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNAseq to characterize gene expression in the same individuals. To quantify regulatory divergence, we compared CRE activity across species by testing differential ChIP-seq read depths directly measured for orthologous sequences. We show that the primate regulatory landscape is largely conserved across the lineage, with 63% of the tested human liver CREs showing similar activity across species. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell-type specificity, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions. We further demonstrate that conserved CREs bind master regulators, suggesting that while CREs contribute to species adaptation to the environment, core functions remain intact. Newly evolved CREs are enriched in young transposable elements (TEs), including Long-Terminal-Repeats (LTRs) and SINE-VNTR-Alus (SVAs), that significantly affect gene expression. Conversely, only 16% of conserved CREs overlap TEs. We tested the cis-regulatory activity of 69 TE subfamilies by luciferase reporter assays, spanning all major TE classes, and showed that 95.6% of tested TEs can function as either transcriptional activators or repressors. In conclusion, we demonstrated the critical role of TEs in primate gene regulation and illustrated potential mechanisms underlying evolutionary divergence among the primate species through the noncoding genome.

SummaryHumans display remarkable inter-individual variation in immune response when exposed to identical immune challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we carried out in-depth genetic, epigenetic, and transcriptional profiling on primary macrophages derived from a panel of European and African-ancestry individuals before and after infection with influenza A virus (IAV). We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to IAV across individuals, and that ancestry-associated differences in gene expression are tightly coupled with variation in enhancer activity. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape are genetically controlled, even more so than variation in gene expression. Lastly, we show that among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, the remaining corresponding to genetic variants that impact one or more epigenetic marks, which stresses the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.

16Gene regulation plays a critical role in the evolution of phenotypic diversity. We investigated 17 the evolution of liver promoters and enhancers in six primate species. We performed ChIP-18 seq for two histone modifications and RNA-seq to profile cis-regulatory element (CRE) 19 activity and gene expression. The primate regulatory landscape is largely conserved across 20 the lineage. Conserved CRE function is associated with sequence conservation, proximity 21 to coding genes, cell type specificity of CRE function, and transcription factor binding. 22 Newly evolved CREs are enriched in immune response and neurodevelopmental functions, 23 while conserved CREs bind master regulators. Transposable elements (TEs) are the 24 primary source of novelty in primate gene regulation. Newly evolved CREs are enriched in 25 young TEs that affect gene expression. However, only 17% of conserved CREs overlap a 26 TE, suggesting that target gene expression is under strong selection. Finally, we identified 27 specific genomic features driving the functional recruitment of newly inserted TEs. 28 29 30 56 With a goal of answering these questions, we collected liver samples from six 57 primate species. Core liver functions are largely conserved across primate species. 58 However, different environmental exposures, diets, and lifestyles likely directed the 59 adaptation of liver functions, and associated regulatory evolution, making this tissue an 60 optimal model in which explore the conservation and divergence of the gene regulation. 61 To characterize primate liver cis-regulatory evolution, we performed chromatin 62 immunoprecipitation followed by sequencing (ChIP-seq) for Histone H3 Lysine 27 63 89 90 91 Results 92 93Data generation, quality assessment, and validation 94 We generated a total of 757 million RNA-seq reads and 1.70 billion ChIP-seq reads 95 (H3K27ac, H3K4me1, and input) from post mortem livers of three or four individuals per 96 3 species of mouse lemur (Microcebus murinus), bushbaby (Otolemur garnettii), marmoset 97 (Callithrix jacchus), rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), and 98

No abstract

No abstract