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Researchers Use CRISPR-based Method to Track RNA In Vivo

NEW YORK (GenomeWeb) – A research team led by researchers from the University of California has modified the CRISPR/Cas9 system to demonstrate the ability to track specific RNA sequences and processes in vivo.

As described in a paper published today in Cell, the investigators were able to use their system to visualize specific RNA molecules accumulating in stress granules — dense aggregations of proteins and RNA that form in the cytosol in response to cellular stress and have been linked to neurodegenerative disorders such as amyotrophic lateral sclerosis. 

They also found that they could use Cas9 to target an mRNA without altering mRNA abundance or the amount of translated protein.

"We are just beginning to see the implications of genome engineering using the CRISPR technology, but many diseases, including cancer and autism, are linked to problems with another fundamental biological molecule: RNA," Gene Yeo, senior study author and an associate professor at the University of California, San Diego, said in a statement.

The researchers began their project based on a modification attempted in the lab of co-author Jennifer Doudna from the University of California, Berkeley. In that study, the researchers found that it was possible to design a protospacer adjacent motif (PAM) as part of an oligonucleotide (PAMmer) which binds to the single-stranded RNA, allowing Cas9 to efficiently recognize and cleave RNA rather than DNA (RCas9). The researchers determined that with a few further modifications, they could use this method to not only recognize RNA instead of DNA but actually track its movements through cells.

Previously, researchers have attempted to use molecular beacons to track RNA sequences, however, these are limited to imaging applications and are difficult to deliver into cells. Researchers have also attempted to use aptamers to enable RNA tracking in living cells, but these are limited in the number of RNA sequences that they can recognize.

CRISPR/Cas9, however, has thus far proved extremely useful in the genome engineering field and the research team thought that it would be an ideal base to create a better RNA tracking tool.

To prove their concept, the team tested whether a dead Cas9 (dCas9) that was tagged with the fluorescent protein mCherry and contained a nuclear localization signal could be co-exported from the nucleus with a messenger RNA in the presence of a single-guide RNA (sgRNA) and PAMmer designed to recognize that specific mRNA.

The experiment succeeded and the researchers were also able to observe accumulation of ACTB, CCNA2, and TFRC mRNAs in RNA granules that correlated with fluorescence in situ hybridization visualization using image analysis software.

Once they had established that their method was effective, the researchers showed that they could use the sgRNA and PAMmer targeting sequences to track mRNA trafficking to stress granules.

The researchers demonstrated that they could take time-resolved measurements of ACTB mRNA trafficking to stress granules over a period of 30 minutes. They noted in the paper that RCas9 was capable of measuring the association of CCNA2 and TFRC mRNA trafficking to stress granules, as well.

Based on their results, the investigators believe they have established RCas9 as a means to track RNA in living cells in a programmable manner that doesn't require genetically encoded tags.

"One potential application of this technique is to track RNA transport in diseased neurons over time in order to identify the molecular features of these diseases and support the developments of therapies," David Nelles, first author on the study and a researcher at the University of California, San Diego, said in a statement. "Just as CRISPR-Cas9 is making genetic engineering accessible to any scientists with access to basic equipment, RNA-targeted Cas9 may support countless other efforts for studying the role of RNA processing in disease or for identifying drugs that reverse defects in RNA processing."