Transcriptomics in the 21st century: a review of achievements and limitations

A transcriptome, being a complete set of RNA molecules transcribed by the genome of a cell or organism at a specific time, is a dynamic and informative object of research in modern biology. Its variability and ability to reflect responses to internal and external stimuli make transcriptome analysis an indispensable tool for understanding fundamental biological processes, developing diagnostic approaches, and applying it to fields such as agriculture, ecology, and biotechnology. Studying the transcriptome makes it possible to identify the differential expression of genes in response to various factors, decipher the molecular mechanisms of disease pathogenesis, identify potential targets for therapeutic intervention, and optimize biotechnological processes. This study presents an analysis of the evolution of transcriptome technologies in the 21st century, covering a range of methodological approaches from traditional gene expression analysis methods, such as reverse transcription followed by polymerase chain reaction (RT-PCR) and microarrays, to modern high-throughput next-generation sequencing (RNA-seq) methods. A comparative assessment of the advantages and disadvantages of each method is provided, with a focus on their specific applications in various fields, including medical diagnostics, agriculture, environmental research, and the food industry. Special attention is paid to discussing the capabilities and limitations of each technology in the context of solving specific problems, such as identifying disease biomarkers, studying the adaptation of organisms to changing environmental conditions, and optimizing biotechnological processes.