Transkriptome

Transkriptome, the German term for transcriptome, refers to the complete set of RNA transcripts produced by the genome under a given condition or in a specific cell type. It encompasses messenger RNA, non-coding RNAs and other RNA species, reflecting gene activity rather than genomic sequence. The transcriptome is tissue- and time-specific and can change in development, health, or disease.

Because transcripts include coding and non-coding RNAs and may exist as multiple isoforms due to alternative splicing, the transcriptome is highly heterogeneous. Transcript abundance spans several orders of magnitude and can be unstable, influenced by technical factors and RNA quality. A key distinction is that the transcriptome provides a functional readout of gene expression, complementing the genome and proteome.

Studying the transcriptome relies on RNA sequencing (RNA-seq), microarrays, or emerging long-read sequencing technologies. RNA-seq is widely used to quantify transcript levels allele-specific expression, detect novel transcripts, and infer alternative splicing events. Long-read platforms improve isoform resolution, while single-cell RNA sequencing reveals heterogeneity across cells. Computational analysis involves alignment to a reference genome, transcript assembly, quantification, and differential expression or differential transcript usage analysis.

Applications include understanding development, tissue specificity, disease mechanisms, and responses to treatment. Data are deposited in public resources such as GTEx, ENCODE, and GEO, enabling cross-study comparisons. Limitations include biases from library preparation, difficulties in accurate isoform quantification, and the need for robust annotation.

The transcriptome is a dynamic, context-dependent layer of biology. It complements the genome and proteome in conveying cellular function and regulation, and its study continues to advance with improvements in sequencing technology and computational methods.