Transcriptomics and Proteomics: Integration?


The protein‐coding genes are transcribed to premessenger ribonucleic acid (pre‐mRNA), further processed to messenger ribonucleic acid (mRNA) and finally translated into protein through several regulated steps. Proteins may be further processed and modified posttranslationally and may interact with each other in complexes. The transcriptome constitutes the complete set of all RNA molecules, coding and noncoding, and the proteome refers to the complete set of proteins that is expressed in an organelle, cell type or tissue under a specific set of conditions. The transcriptome is studied with transcriptomics, a set of high‐throughput methods giving information on sequence and abundance of transcripts. The proteome is studied with proteomics, a set of techniques developed to approach a high‐throughput level providing identification of proteins, their expression levels and posttranslational modifications. The two disciplines each provide unique information and supplement each other, and changes in transcript levels may not necessarily correspond to similar changes in protein levels.

Key Concepts

  • Differential expression transcriptomics is used to analyse fold‐changes of transcripts (mRNA) between groups of comparable samples using DNA array technology.
  • Bottom‐up proteomics is used to identify and quantify proteins in complex samples after digesting with an enzyme, usually trypsin, before mass spectrometry analysis.
  • Top‐down proteomics is used to analyse proteins by mass spectrometry without enzymatic digestion.
  • Differential expression proteomics is used to analyse protein fold‐changes between groups of comparable samples.
  • Interactomics is used to map physical and functional protein–protein interactions (PPI) based on a wide variety of approaches, including biochemical and biophysical techniques as well as bioinformatics.

Keywords: transcriptome; transcriptomics; proteome; proteomics; DNA array; 2D‐PAGE; LC–MS/MS; posttranslational modifications; interactomics

Figure 1. Flow of information from DNA via mRNA to protein. A gene (DNA) is transcribed (step 1) to the various forms of RNA, first to pre‐mRNA that may be edited (step 2) and then processed (step 3) to one or by alternative splicing to several forms of mRNAs. The mRNAs are then transported (step 4) out of the nucleus to the cytosol. In the cytosol, the mRNA may be degraded (step 5) or translated (step 6) into protein. The activities of the proteins are controlled (step 7). They may be synthesised as inactive proteins that later are reversibly or irreversibly activated, or alternatively synthesised as active proteins that later are inactivated. Proteins are the ultimate effecting molecules producing the physiologic effect (step 8) in virtually every mechanism in the cell.


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Ludvigsen, Maja, and Honoré, Bent(Apr 2018) Transcriptomics and Proteomics: Integration?. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0006188.pub2]