SHAPESeq

SHAPESeq is a high-throughput sequencing method used to study the structure and function of non-coding RNAs, particularly microRNAs (miRNAs). It combines the Selective 2'-hydroxyl Acylation analyzed by Primer Extension (SHAPE) method with next-generation sequencing (NGS) technology. The SHAPE method uses chemical reagents to modify the RNA structure, creating a map of the RNA's secondary structure. This map is then sequenced using NGS, allowing for the simultaneous analysis of thousands of RNA molecules.

SHAPESeq provides several advantages over traditional SHAPE methods. It enables the analysis of large numbers of RNA molecules, providing a more comprehensive understanding of RNA structure and function. It also allows for the identification of structural variations and the analysis of RNA structure in different cellular contexts. Additionally, SHAPESeq can be used to study the structure of RNA-protein complexes, providing insights into the role of proteins in RNA folding and function.

The SHAPESeq method involves several steps. First, the RNA of interest is modified using SHAPE reagents. The modified RNA is then ligated to adapters and sequenced using NGS. The sequencing data is analyzed to generate a map of the RNA's secondary structure. This map can be used to identify structural features, such as base pairing and loops, and to compare the structure of different RNA molecules.

SHAPESeq has been used to study a wide range of non-coding RNAs, including miRNAs, long non-coding RNAs (lncRNAs), and small interfering RNAs (siRNAs). It has provided insights into the structure and function of these RNAs, as well as their role in various biological processes, such as gene regulation and disease. The method has also been used to study the structure of RNA-protein complexes, providing insights into the role of proteins in RNA folding and function.