RNA Granules: A View from the RNA Perspective

Abstract

<jats:p>RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given to the proteins that form these condensates and thus many fundamental questions about the biology of RNA granules remain poorly understood: How and which RNAs enrich in RNA granules, how are transcripts regulated in them, and how do granule-enriched mRNAs shape the biology of a cell? In this review, we discuss the imaging, genetic, and biochemical data, which have revealed that some aspects of the RNA biology within granules are carried out by the RNA itself rather than the granule proteins. Interestingly, the RNA structure has emerged as an important feature in the post-transcriptional control of granule transcripts. This review is part of the Special Issue in the Frontiers in RNA structure in the journal Molecules.</jats:p>

Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes

“…We show that in vivo CP-puncta only form in bacterial cell poles. The puncta survive cell lysis, and in vitro a mix of the same RNA and proteins form similar puncta that are consistent with current understanding of RNP granule formation and phase transition models (Tian et al, 2020). By tracking puncta fluorescent signals in vivo , we demonstrate that for all slncRNA molecules used in our experiment, the various puncta emitted similar signals characterized by bursts of increasing or decreasing fluorescent intensity.…”

Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles

“…Condensates at cell membranes ( 81 ) and in the cytosol have been shown to regulate cell division, migration and invasion ( 82 , 83 ), transgenerational memory ( 84 , 85 , 86 ), and immunomodulation ( 87 ) in response to a variety of morphogens and endo/para/autocrine signals. In addition to acting across a range of timescales, condensation in response to external perturbations plays a critical role in shaping the spatial organization of cells by moving RNAs and proteins into dynamic MLOs with complex organization, suggesting an intimate relationship between macromolecular sequence, intracellular organization, and the extracellular environment ( 66 , 88 , 89 , 90 ).…”

Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation

“…RBPs are of great importance in RNA–protein interactions, which are characterized by the recognition of a specific sequence or structural element in the target RNA by an RNA-binding domain (RBD) such as an RRM or K homology domain [ 139 ]. In addition, RBPs appear frequently in LLPS [ 140 ]; the sequence-binding specificity of different RBDs may determine the processing of a certain subset of nascent RNAs in a particular droplet. High-throughput studies have shown that the RNA-binding proteomes of plants can be divided into three categories: RBPs containing classical RBDs (22%), RBPs containing non-classical RBDs (39%), and RBPs containing unknown RBDs (39%) [ 141 ].…”