A new RNA sequencing method has been developed that has been used to identify numerous modified small RNAs that have, until now, not been possible to detect.
RNA plays an essential role in decoding DNA, acting as an intermediate molecule in the synthesis of proteins. There are many different RNA molecules present inside cells, including ribosomal RNA (rRNA) and transfer RNA (tRNA), which are involved in protein synthesis.
Small RNA molecules, such as MicroRNA, piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), and RNA-derived small RNA (rsRNA), are essential to health and play a role in diseases such as cancer and diabetes. These small RNA molecules are often modified by various chemical groups which changes their functions.
High-throughput sequencing of RNA in biological samples has helped to identify many small RNA populations in cells, each of which plays a role in gene expression and protecting genomes, but many of these molecules cannot be detected using traditional RNA sequencing methods. It is therefore not known how many modified RNAs are present in biological samples and, if they cannot be detected, it is impossible to know what their functions may be and the role they play in health and disease.
The new RNA sequencing method developed by researchers at the University of California, Riverside could help to discover new small RNA molecules and allow them and their roles to be studied. The technique has been named Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing (PANDORA-seq).
“PANDORA-seq can be widely used to profile small RNA landscapes in various physiological and disease conditions to facilitate the discovery of key regulatory small RNAs involved in these conditions,” said Qi Chen, assistant professor of biomedical sciences at the UCR School of Medicine and lead researcher of the study.
Chen explained that small RNAs often wear an invisibility cloak which prevents them from being detected by standard RNA sequencing methods. PANDORA-seq involves a stepwise enzymatic treatment that removes key RNA modifications which essentially removes that invisibility cloak and allows the small RNA molecules to be detected.
Previously, the small RNA landscape was thought to be dominated by microRNAs; however, PANDORA-seq has shown that is not the case. It is actually tsRNAs and rsRNAs that dominate the small RNA landscape.
“With PANDORA-seq, we found unprecedented microRNA/tsRNA/rsRNA dynamics when somatic cells are reprogrammed to induced pluripotent stem cells, which are generated by adult cells and have properties similar to those of embryonic stem cells, making them capable of differentiating into all cell types of the body. Some tsRNAs and rsRNAs can impact protein synthesis and even affect embryonic stem cell lineage differentiation in embryonic stem cells,” said UCR assistant professor of Biochemistry and corresponding author, Sihem Cheloufi.
The researchers will now investigate how these tsRNAs and rsRNAs are generated, how they function in stem cells, and how they determine cell fate decisions during development.
You can read more about the study in the paper – PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications – which was recently published in the Nature Cell Biology. DOI: 10.1038/s41556-021-00652-7