Transcriptomics methods are being improved
A few cells are enough for an RNA portrait of a tissue
Kirill Stasevich, Compulenta
Many have heard the word "genome": it refers to the totality of hereditary material contained in an organism's cell, or, roughly speaking, everything contained in DNA. In addition to the genome, however, there is also a transcriptome, and this is already a less well-known thing. But not among scientists, who are interested in transcriptome more and more every day.
Schematic representation of transcription: the enzyme RNA polymerase synthesizes RNA
on the DNA template from the starting point to the stop signal. (Figure aymanz.13.)Recall: information from DNA is first translated into RNA molecules during transcription.
Therefore, as it is easy to guess, a transcriptome is called the whole set of RNAs "planed" by enzyme complexes of DNA-dependent RNA polymerases. The quantity and quality of RNA can say a lot about the state of a cell: which ones work poorly, which ones work well (and how well), and which ones are silent at all. In addition, a huge layer of genetic regulation falls precisely on the transcription of RNA, on splicing and on the processes that determine the time of its life in the cell. The cell solves certain problems that require quick action, again at the RNA level, since its molecules are much easier to handle.
In fact, a transcriptome is something like a freeze frame from the life of a cell, it allows you to detail molecular processes and, therefore, to understand them better.
However, when analyzing transcriptomes, there are great difficulties of a purely methodological nature. Firstly, different RNAs in a cell exist in very different quantities, and, say, the RNA of some cancer protein can easily be lost against the background of ribosomal RNA, which is innumerable. Meanwhile, even a small excess of oncoRNA is fraught with serious troubles. Secondly, RNA is isolated from cells for analysis, and here again the same problem: several malignant cells can be lost against the background of an abundance of quite healthy cells.
RNA molecules lengthening during their synthesis on a DNA template
(illustration by Visuals Unlimited / Corbis).Researchers from the University of California at San Diego (USA) have come up with a method by which both difficulties can be solved.
As scientists write in Nature Scientific Reports (Bhargava et al., Quantitative Transcriptomics using Designed Primer-based Amplification), their method allows you to "see" 50 pg (picogram – one trillionth of a gram) of RNA, that is, it is enough to take 50-100 cells for analysis, and you don't have to worry that numerous unnecessary The RNA will obscure the small necessary one from us.
In the method of Shankar Subramaniam (Shankar Subramaniam) and his colleagues, you can specifically focus on a certain type of RNA or its fragment, where, perhaps, some mutation is hidden. Such focusing allowed, for example, to see the activity of RNA genes at the early stages of the development of mouse embryonic cells, which until now scientists had observed only at later stages: before that, the molecules of the necessary RNA were indistinguishable in the thick of ribosomal RNAs. In addition, according to the authors of the work, the method is faster and more economical, which gives it an advantage over other similar technologies that have appeared recently.
Transcriptome analysis, which allows, as under a magnifying glass, to purposefully examine certain molecules, certainly has a wonderful future both in fundamental science and in clinical medicine. However, when planning the medical prospects of such scientific achievements, it is necessary, as usual, to consider them in the context of the medical budget: after all, not every medical institution can afford the latest biotechnological novelties.
Prepared based on the materials of the University of California, San Diego –
Bioinformatics Breakthrough: High Quality Transcriptome from as Few as Fifty Cells.
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