Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

Nature Biotechnology

10.1038/s41587-021-00949-w

http://dx.doi.org/10.1038/s41587-021-00949-w

Ploy N. Pratanwanich, Fei Yao, Ying Chen, Casslynn W. Q. Koh, Yuk Kei Wan, Christopher Hendra, Polly Poon, Yeek Teck Goh, Phoebe M. L. Yap, Jing Yuan Chooi, Wee Joo Chng, Sarah B. Ng, Alexandre Thiery, W. S. Sho Goh, Jonathan Göke

19 July 2021

Pratanwanich, P. N., Yao, F., Chen, Y., Koh, C. W. Q., Wan, Y. K., Hendra, C., Poon, P., Goh, Y. T., Yap, P. M. L., Chooi, J. Y., Chng, W. J., Ng, S. B., Thiery, A., Goh, W. S. S., Göke, J. (2021). Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nature Biotechnology, 39(11), 1394–1402. https://doi.org/10.1038/s41587-021-00949-w

RNA modifications, such as N6-methyladenosine (m6A), modulate functions of cellular RNA species. However, quantifying differences in RNA modifications has been challenging. Here we develop a computational method, xPore, to identify differential RNA modifications from nanopore direct RNA sequencing (RNA-seq) data. We evaluate our method on transcriptome-wide m6A profiling data, demonstrating that xPore identifies positions of m6A sites at single-base resolution, estimates the fraction of modified RNA species in the cell and quantifies the differential modification rate across conditions. We apply xPore to direct RNA-seq data from six cell lines and multiple myeloma patient samples without a matched control sample and find that many m6A sites are preserved across cell types, whereas a subset exhibit significant differences in their modification rates. Our results show that RNA modifications can be identified from direct RNA-seq data with high accuracy, enabling analysis of differential modifications and expression from a single high-throughput experiment.

Publisher Copyright

This research is supported by core funding from: A*STAR
Grant Reference no. : NA

This research / project is supported by the National Medical Research Council - Individual Research Grant funding scheme
Grant Reference no. : OFIRG20nov-0108

This research / project is supported by the Thailand Research Fund - N/A
Grant Reference no. : RTA6080013

This is a post-peer-review, pre-copyedit version of an article published in Nature Biotechnology. The final authenticated version is available online at: http://dx.doi.org/10.1038/s41587-021-00949-w.

https://oar.a-star.edu.sg/communities-collections/articles/20350

1087-0156
1546-1696

Genome Institute of Singapore