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

Abstract

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.

• Authors: 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
• Journal: Nature biotechnology (Nat Biotechnol) Vol. 39 Issue 11 Pg. 1394-1402 (11 2021) ISSN: 1546-1696 [Electronic] United States
• PMID: 34282325 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

Chemical References

• RNA

Topics

• High-Throughput Nucleotide Sequencing
• Humans
• Nanopore Sequencing
• Nanopores
• RNA (genetics, metabolism)
• RNA Processing, Post-Transcriptional (genetics)
• Sequence Analysis, RNA (methods)
• Transcriptome (genetics)