Wang, J., Yang, L., Cheng, A., Tham, C.-Y., Tan, W., Darmawan, J., de Sessions, P. F., Wan, Y. (2024). Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome. Nature Communications, 15(1). https://doi.org/10.1038/s41467-023-44656-3
Abstract:
Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low-abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selectively deplete and enrich RNAs of interest without biochemical manipulation before sequencing. Adaptive sampling performed on a pool of in vitro transcribed RNAs resulted in a net increase of 22-30% in the proportion of transcripts of interest in the population. Enriching and depleting different proportions of the Candida albicans transcriptome also resulted in a 11-13.5% increase in the number of reads on target transcripts, with longer and more abundant transcripts being more efficiently depleted. Depleting all currently annotated Candida albicans transcripts did not result in an absolute enrichment of remaining transcripts, although we identified 26 previously unknown transcripts and isoforms, 17 of which are antisense to existing transcripts. Further improvements in the adaptive sampling of RNAs will allow the technology to be widely applied to study RNAs of interest in diverse transcriptomes.
License type:
Attribution 4.0 International (CC BY 4.0)
Funding Info:
This research / project is supported by the A*STAR - CDA grant (202D8067)
Grant Reference no. : C210112013
This research is supported by the A*STAR Investigatorship, National Research Foundation of Singapore, EMBO Young Investigatorship and CIFAR Azrieli global scholar fellowship