Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome

Jiaxu Wang, Lin Yang, Anthony Cheng, Cheng-Yong Tham, Wenting Tan, Jefferson Darmawan, Paola Florez Sessions () and Yue Wan ()
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Jiaxu Wang: Genome Institute of Singapore, A*STAR
Lin Yang: Oxford Nanopore Technologies
Anthony Cheng: Genome Institute of Singapore, A*STAR
Cheng-Yong Tham: Oxford Nanopore Technologies
Wenting Tan: Genome Institute of Singapore, A*STAR
Jefferson Darmawan: Genome Institute of Singapore, A*STAR
Paola Florez Sessions: Oxford Nanopore Technologies
Yue Wan: Genome Institute of Singapore, A*STAR

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-023-44656-3

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