DRUMMER-rapid detection of RNA modifications through comparative nanopore sequencing

被引:31
作者
Abebe, Jonathan S. [1 ]
Price, Alexander M. [2 ]
Hayer, Katharina E. [3 ]
Mohr, Ian [1 ]
Weitzman, Matthew D. [2 ,4 ]
Wilson, Angus C. [1 ]
Depledge, Daniel P. [1 ,5 ,6 ]
机构
[1] NYU, Sch Med, Dept Microbiol, New York, NY 10016 USA
[2] Childrens Hosp Philadelphia, Dept Pathol & Lab Med, Div Protect Immun, Philadelphia, PA 19104 USA
[3] Childrens Hosp Philadelphia, Dept Biomed & Hlth Informat, Philadelphia, PA 19104 USA
[4] Univ Penn, Dept Pathol & Lab Med, Perelman Sch Med, Philadelphia, PA 19104 USA
[5] Hannover Med Sch, Inst Virol, Hannover, Germany
[6] German Ctr Infect Res DZIF, Partner Site Hannover Braunschweig, Hannover, Germany
关键词
D O I
10.1093/bioinformatics/btac274
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides. Results: DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity.
引用
收藏
页码:3113 / 3115
页数:3
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