Title |
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data
|
---|---|
Published in |
BMC Bioinformatics, November 2015
|
DOI | 10.1186/s12859-015-0800-0 |
Pubmed ID | |
Authors |
Sara R. Selitsky, Praveen Sethupathy |
Abstract |
Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are no methods for accurate annotation and quantification of these small RNAs. tRNA-derived RNAs have unique features that limit the utility of conventional alignment tools and quantification methods. We describe here the challenges of mapping, naming, and quantifying tRNA-derived RNAs and present a novel method that addresses them, called tDRmapper. We then use tDRmapper to perform a comparative analysis of tRNA-derived RNA profiles across different human cell types and diseases. We found that (1) tRNA-derived RNA profiles can differ dramatically across different cell types and disease states, (2) that positions and types of chemical modifications of tRNA-derived RNAs vary by cell type and disease, and (3) that entirely different tRNA-derived RNA species can be produced from the same parental tRNA depending on the cell type. tDRmappernot only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel tRNA and tRNA-derived RNA biology. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Italy | 1 | 14% |
France | 1 | 14% |
Unknown | 5 | 71% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 4 | 57% |
Members of the public | 2 | 29% |
Practitioners (doctors, other healthcare professionals) | 1 | 14% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Germany | 1 | 1% |
South Africa | 1 | 1% |
United Kingdom | 1 | 1% |
Denmark | 1 | 1% |
Spain | 1 | 1% |
United States | 1 | 1% |
Unknown | 88 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 22 | 23% |
Student > Ph. D. Student | 21 | 22% |
Student > Master | 13 | 14% |
Student > Doctoral Student | 6 | 6% |
Student > Bachelor | 6 | 6% |
Other | 7 | 7% |
Unknown | 19 | 20% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 30 | 32% |
Biochemistry, Genetics and Molecular Biology | 29 | 31% |
Medicine and Dentistry | 4 | 4% |
Computer Science | 3 | 3% |
Neuroscience | 2 | 2% |
Other | 5 | 5% |
Unknown | 21 | 22% |