How do transcribed enhancers confer genetic risk in Amyotrophic Lateral Sclerosis?

Spatial interactions between transcriptional regulatory elements establish gene regulatory networks. Enhancers are fundamental to such regulatory networks, conferring precise spatiotemporal gene expression patterns. Thus, it is not surprising that variation within enhancers may underpin the genetic architecture of disease. In fact, the vast majority of single nucleotide polymorphisms (SNPs) associated with human complex diseases map to the non-coding genome, with causal disease variants particularly enriched within enhancers. The transcription of enhancer RNAs (eRNAs), the non-coding RNA species encoded from active enhancers, is a key factor contributing to enhancer activity. Not only may enhancer transcription data provide insight into how enhancer activity changes upon mutation, but enhancers containing disease-associated variants may yield aberrant eRNAs capable of disrupting transcriptional regulation to culminate in disease phenotype.

By mapping putative Amyotrophic Lateral Sclerosis (ALS)-associated enhancers, we evaluate their activity by assessing chromatin accessibility, enhancer-associated chromatin modifications, and eRNA transcription, in the context of disease. By employing epigenomic and transcriptomic analyses, coupled with reporter assays to assess the impact of ALS-associated SNPs, we gain insights into the transcriptional and regulatory consequences of disease-associated SNPs on enhancer function. Using computational RNA structure prediction, enhancers containing ALS-associated variants are predicted to yield eRNAs with altered structure, and therefore potentially function. In disease contexts, we further explore how both distal and intragenic ALS-associated enhancers affect not only gene expression but differential messenger RNA (mRNA) isoform expression. Therefore, investigating the effects of ALS-associated SNPs on enhancer activity, eRNA expression and eRNA structure not only provide great insights into the pathogenic mechanisms underlying sporadic ALS, but may also contribute to a broader understanding of how eRNAs function independently from their associated enhancers.