High‐Throughput Analysis of RNA Structure by SHAPE Chemistry

Abstract

Single‐stranded RNA viruses encompass a broad class of infectious agents and, in their diverse forms, cause the common cold, cancer, AIDS, and many other serious health threats. Viral replication is regulated at many levels, including using essential, conserved genomic RNA structures to exploit and circumvent host biology. However, the vast majority of potential regulatory elements within viral RNA genomes are uncharacterized. We use high‐throughput SHAPE (selective 2′‐hydroxyl acylation analyzed by primer extension) to quantify RNA backbone flexibility at single nucleotide resolution and from which robust structural information can be immediately derived. We detect specific protein‐RNA interactions inside HIV virions and identify three RNA binding functions for the viral nucleocapsid protein. Analysis of the structure of an entire, authentic, ~9,200 nucleotide HIV‐1 genome at single nucleotide resolution reveals that the HIV‐1 genome, and potentially most large coding RNAs, is punctuated by numerous previously unrecognized, but conserved, RNA regulatory motifs. High‐throughput SHAPE reveals a comprehensive view of HIV‐1 RNA genome structure and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome.