Multilevel effects of non-coding genetic variation on regulatory elements and chromatin organization. chromatin analyses in rats

Background: Genetic variation associated with complex disease is often located outside protein-coding genes where it may affect regulatory mechanisms. Gene expression is regulated by many different mechanisms making interpretation of non-coding variation remains challenging. Although promoter elements and transcription factor binding are increasingly understood, we systematically analyzed the effects of genetic variation on variability in enhancer activity and three-dimensional (3D) chromatin organization in relation to gene expression levels in ten inbred rat strains. Results: We find that both nucleotide and structural genetic variants are associated with changes in enhancer acetylation and nearby gene expression level differences. Chromatin organization was largely conserved between genetic backgrounds. Interestingly, we show that chromatin regions that are differentially organized are enriched for single nucleotide and larger structural genetic variants and that these regions correspond strongly with differences in enhancer activity. However, this did not result in local gene expression changes. Conclusions: Our findings demonstrate that genetic variation influences gene expression through multiple regulatory mechanisms, including enhancer activity and 3D chromatin structure. We illustrate why multilevel analyses are required to properly understand the functional effects of non-coding variants.