Spatial translatomics pinpoints protein production in cells

Spatial transcriptomics, which can show where RNA is located within cells, has exploded in popularity in recent years. But because cells control translation tightly, the correlation between messenger RNA (mRNA) and protein is not perfect.

To better understand the relationship between RNA levels and the proteins they encode, researchers led by Xiao Wang at the Massachusetts Institute of Technology have developed a method for spatial ribosome profiling that can detect mRNA being translated (Science 2023, DOI: 10.1126/science.add3067). The method, called RIBOmap, relies on DNA probes designed to amplify only the messenger RNAs that are bound to ribosomes. The technique can show where hundreds of genes are being translated in a single cell.

The researchers validated their method by comparing their new spatial translatomes to spatial transcriptomic data and to protein locations determined with antibodies or through bulk protein identification using mass spectrometry. “Current MS-based imaging often lacks single-cell resolution,” Wang says in an email.

The team found that the translatome aligns closely with known protein locations in complex tissues like the brain. Besides giving information about what proteins are present and where, RIBOmap enables large-scale study of gene regulation. For example, the researchers found that individual subunits of large protein complexes tend to be translated in the same area in cells, which Wang says had been seen only in isolated cases.

When combined with transcriptomics, the method can spot areas in the brain of a mouse where translation levels change even though the amount of mRNA remains the same, suggesting that specific cells control translation differently. Wang says that understanding such differences in regulation is a key future direction for her lab.

In a commentary accompanying the paper, Rong Fan, a biomedical engineer at Yale University, notes that one drawback to RIBOmap is that it is probe based, meaning that researchers must specify a panel of mRNAs to be detected (Science 2023, DOI: 10.1126/science.adi6844). But Fan also notes that the basic detection strategy RIBOmap uses could be adapted to study other stages of RNA regulation. For example, the probes could be redesigned to bind to an exonuclease instead of a ribosome to investigate RNA turnover.