Published: 22-12-2013 11:00 | Updated: 29-10-2014 10:02

"Barcodes" help researchers measure gene activity

Researchers at Karolinska Institutet have developed a new method for measuring gene activity in single cells, which is more sensitive and accurate than previous ways of measurement. This new method, which is presented in the journal Nature Methods, is based on a form of molecular "barcodes", providing each mRNA molecule with a distinct label.

Because body tissue consists of many different cell types, researchers need to be able to analyze single cells separately. For example, in a tumor there could be a small number of stem cells driving the development of tumor growth. If the whole tumor is analyzed, there is a great risk that the stem cells will pass undetected. However, if each cell from the tumor is analyzed it is possible to observe both stem cells, and more specialized cells.

When a gene is activated, a copy of the gene is generated in the form of a messenger RNA molecule (mRNA), which then functions as a template in the production of different proteins. Patterns of gene activity decide what kind of cell type is produced, but may also explain disease development. The gene activity is usually analyzed by measuring the levels of mRNA in the tissue. However, until now it has been difficult to study mRNA in single cells, as there are only a hand-full of such molecules in each cell.

A group of researchers at Karolinska Institutet, led by Associate Professor Sten Linnarsson, therefore developed a form of molecular "barcode system", where each mRNA molecule is labeled with a unique DNA sequence. It then becomes possible for researchers to copy those few mRNA molecules in single cells thousands of times, and yet be able to track the exact numbers of molecule present in the cell from the start just by counting the different barcodes or labels. Copying is necessary, because current measurement instruments are unable to detect small numbers of mRNA molecules.

This work was supported by grants from the Swedish Research Council, the European Research Council, the Swedish Cancer Society, and the Ragnar Söderberg Foundation.

More about the Linnarsson Lab


Quantitative single-cell RNA-seq with unique molecular identifiers
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg & Sten Linnarsson
Nature Methods, advance online publication 22 December 2013, doi:10.1038/NMETH.2772