High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation

The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary structures. The roles of DNA and RNA secondary structures in transcriptional regulation remain incompletely understood. However, advances in high-throughput assays have enabled genome wide characterization of some secondary structures. Here, we describe their regulatory functions in promoters and 3'UTRs, providing insights into key mechanisms through which they regulate gene expression. We discuss their implication in human disease, and how advances in molecular technologies and emerging high-throughput experimental methods could provide additional insights.

Automated summary

The canonical right-handed double helix structure of DNA, known as B DNA, is the most stable form. However, non-canonical secondary structures can also form under specific environments and sequence motifs. The roles of these secondary structures in transcriptional regulation are not fully understood, but recent advancements in high-throughput assays have allowed for genome-wide characterization of some secondary structures. This article discusses their regulatory functions in promoters and 3'UTRs, their implications in human disease, and the potential insights that can be gained through molecular technologies and high-throughput experimental methods.