RNA in cells [chapter]

Valeria de Turris, Robert H. Singer
Single Molecule Dynamics in Life Science  
In terms of movements and interactions, RNA is one of the most dynamic and flexible molecules in the cell. These characteristics are the keys to understanding its biological roles, in particular in terms of regulation of gene expression. In the cell, the expression of a gene is controlled at different levels. Checkpoints are spread out all along the way, from the triggering of a signal to open the chromatin until posttranslational modifications and degradation of the protein. In this complex
more » ... work, RNA occupies a central position since it is the messenger (mRNA) sent from the site of information storage (DNA in the nucleus) to everywhere in the cell. Some RNA molecules are coding RNAs, read by the ribosome in the cytoplasm to produce functional proteins by ordered loading of the correct amino acids. Other functional RNAs are never translated into proteins (non-coding RNAs, ncRNAs). They can be involved in ribosome assembly and function, such as ribosomal RNA (rRNA), transfer RNA (tRNA) and the small nucleolar RNA (snoRNA); others are implicated in splicing pieces of mRNA together, as are small nuclear RNAs (snRNAs) important components of the spliceosome, the macro-complex that accomplishes this splicing. Moreover, in the last few years new classes of regulatory non-coding RNAs have been discovered: small interfering RNAs (siRNAs) and microRNAs (miRNAs). These ncRNAs are characterized by their tiny dimensions (varying between 21 and 24 nucleotides) and new members are continuously being found. They are involved in multiple functions, from the protection against parasitic nucleic acids, such as viruses and transposons [1], to the control of the expression of specific mRNAs in development and cancer [2] . The discovery of these new RNAs that has strongly improved our understanding of cell defense and regulation also provides tools to manipulate and study gene expression. The relevance of this finding is evident from the 2006 Nobel Prize where Fire and Mello shared the Medicine Prize for the discovery of RNA interference by these small RNAs. Another important characteristic of RNA molecules is that they are never naked in the cell. They are always associated with proteins, forming ribonucleoprotein particles (RNPs). As a consequence, the RNP is much higher in molecular weight than the RNA alone. Moreover, the composition of the complex is modified over time due to exchange of binding partners, therefore increasing the complexity and the spectrum of possible interactions and functions. These characteristics make the RNA molecule, in all its forms and functions, an exciting and important object of study. Many questions have been raised about RNP dynamics in the nucleus and in the cytoplasm. Some of them concern how RNAs move, whether they follow rules of free diffusion or energy-dependent movement, and to what extent the environment, such as chromatin in the nucleus or filament networks in the cytoplasm, constrains RNA movements. RNA dynamics range from the sites of nuclear transcription, where maturation occurs, to the specific localization of particular RNAs in the cytoplasm, which creates defined gradients by enrichment in, or exclusion from, particular areas. 8.2 RNA Visualization inside Cells 172j 8 RNA in cells 176j 8 RNA in cells
doi:10.1002/9783527626137.ch8 fatcat:xpvltoxgrbezphlkufyaenkudu