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Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
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Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
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Journal Article
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
2021
Overview
RNA modifications, such as
N
6
-methyladenosine (m
6
A), 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 m
6
A profiling data, demonstrating that xPore identifies positions of m
6
A 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 m
6
A 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.
m
6
A RNA modifications are quantified in cancer patient samples and cell lines using nanopore sequencing.
Publisher
Nature Publishing Group US,Nature Publishing Group
