Measuring protein production in individual cells

Every cell in the body contains approximately two meters of DNA. This DNA encodes the information to make proteins, which are the main functional molecules in the cell. To produce proteins, the DNA is first copied through a process called transcription, resulting in messenger RNA (mRNA). This mRNA is then translated into proteins by ribosomes, the protein factories of cells. As one of the main steps in this flow of information, it is important to understand how translation is regulated throughout dynamic biological processes and between different types of cells.

Ribosome profiling

A powerful existing technique called ribosome profiling is able to measure the process of translation. However, it currently requires millions of cells to be collected to perform the measurement. This limitation has severely restricted the systems to which ribosome profiling could be applied, making it impractical to study highly dynamic systems and rare types of cells.

Single-cell ribosome profiling

By directly integrating the different steps necessary to perform ribosome profiling, researchers from the group of Alexander van Oudenaarden now developed a method that allows ribosome profiling in individual cells. Combined with a machine learning approach, this technique provides single-codon resolution on genome-wide measurements of ribosome activity in individual cells. In other words, this allows them to study the translational process in each cell individually.

Enteroendocrine cells

To validate and demonstrate the capabilities of this new technology, they studied how translation dynamics change during the different phases of the cell cycle. Additionally, using their new technique, the researchers were able to profile enteroendocrine cells – a very rare cell type that produces and releases hormones in response to nutrient stimuli – in the mouse intestine. “We are excited to start to apply this technique to other systems, for example to study how the translational regulation changes through development”, says Michael VanInsberghe, first author of the study.

Differences between cells

The new ribosome profiling method provides the first steps towards determining the contribution of the translational process to the astonishing diversity between seemingly identical cells.

Publication

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing. Michael VanInsberghe, Jeroen van den Berg, Amanda Andersson-Rolf, Hans Clevers & Alexander van Oudenaarden, Nature (2021).