Long Non-coding RNAs in a Single-Cell Type: Function and Subcellular Localization

After the conclusion of the human genome project, the annotated genes varied among 26,000 and 39,000. However, this gene count is significantly smaller than what was observed later in 2012 when it was evidenced that most of the human genome is transcribed. The vast majority of the transcribed genome does not code for translated RNAs that are involved in the protein synthesis, but comprises non-coding RNAs. This is true not only for the human genome but also for most of the mammalian genomes. Among non-coding RNAs, the most abundant are long non-coding RNAs (lncRNAs). They are emerging as important players in the regulation of several aspects of cellular biology. For instance, they are involved in cell differentiation, normal functioning of differentiated cells, and also involved in the development of pathological conditions such as tumors. They present an expression that is more cell-specific than coding RNAs and for this reason, it is important to study them in single cells instead of using bulk tissues or a cell population. Recent improvements in techniques that allow genomic and transcriptomic analyses of single cells and those for fluorescence amplification have given a considerable boost in the comprehension of cell specificity, subcellular localization, and function of lncRNAs. The purpose of this chapter is to discuss different methods that are available to detect RNA expression using a single cell approach evidencing the advantages and disadvantages of each of them. We will consider how the analysis of single cells has contributed to the better comprehension of lncRNA functions and how it was involved in proposing new paradigms. To conclude the chapter, we will consider published databases to retrieve information on genomic and transcriptomic experiments on single cells