Functional insights into long non-coding and circular RNAs afforded by studying their endogenous interactions with proteins

Improved annotation of eukaryotic genomes has led to the discovery of a myriad of non-coding RNAs (ncRNAs), out of which many are expressed in a tissue- and developmental stage-specific manner. The non-coding fraction of the transcriptome is involved in gene expression regulation at the transcriptional and post-transcriptional levels. These regulatory functions are rarely executed by RNA alone, and most often RNA teams up with proteins to form bigger and dynamic complexes. RNA-binding proteins (RBPs) associate with RNA throughout virtually the entire life cycle of transcripts, from their nascent form until their decay. RNA-protein interactions are dynamic and may influence both constituents with respect to their activity, stability, subcellular organization and localization. Here, we summarize key methods that can be successfully applied to study RNA-protein complexes in vivo. Particularly, we focus on how these approaches help reveal the functions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). Recognizing when and how ncRNA-RBP complexes are formed in the context of endogenous macromolecules enhances our understanding of how ncRNAs employ different mechanisms of action to regulate molecular processes in mammalian cells.