Chapter 13 - Interactions of Proteins with Specific Sequences in RNA

Abstract

This chapter focuses on interactions of proteins with specific sequences in Ribonucleic acid (RNA). The chapter describes several procedures for identifying target RNA(s) for proteins. Many of these methods are used successfully to find the ligands for known RNA binding proteins, such as recognition motifs (RRM) family members. It may be unnecessary to perform combinatorial random RNA selection if the protein is the homolog of an RNA binding protein whose target is identified. In this case, one could proceed directly to the analysis of binding to labeled transcripts of natural RNA sequences. The procedures for identifying minimal binding sites may be of interest to investigators who wish to pursue structural as well as functional analysis of their proteins of interest. It is proposed that many cellular proteins interact with RNAs in vivo as part of homeostatic regulatory networks. The methods described allow the elucidation of such interactions using genomically encoded cellular RNAs for binding to any protein, including antibodies. The chapter discusses about the selection of specific sequences from random RNA libraries, by RNA binding proteins as a first step in identification of in vivo targets. The chapter also explains binding of protein to sequences in cellular RNAs. Determination of minimal binding sequences within RNA ligands is also discussed in detail.