A high-resolution map of the human small non-coding transcriptome
Abstract
Motivation: Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome. Results: In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On the basis of these regions, we found that among the known small non-coding RNA classes, microRNAs were the most prevalent. In subsequent steps, we characterized variations of miRNAs and performed a staged validation of 11 877 candidate miRNAs. Of these, many were actually expressed and significantly dysregulated in lung cancer. Selected candidates were finally validated by northern blots. Although isolated miRNAs could still be present in the human genome, our presented set likely contains the largest fraction of human miRNAs. Supplementary information: Supplementary data are available at Bioinformatics online.
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87 out of 473 novel miRNA were previously reported within other studies.
“We also found that 87 out of 473 novel miRNA were previously reported within other studies (48–52)”
From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [49]
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Cites
Distribution of miRNA expression across human tissues
Ludwig, N., Leidinger, P., Becker, K., Backes, C., Fehlmann, T., Pallasch, C., Rheinheimer, S., Meder, B., Stähler, C., Meese, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw116 · Cited by 968 · see citing works
Self-citationNONCODE 2016: an informative and valuable data source of long non-coding RNAs
Zhao, Y., Li, H., Fang, S., Kang, Y., wu, W., Hao, Y., Li, Z., Bu, D., Sun, N., Zhang, M. Q., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1252 · Cited by 643 · see citing works
Londin, E., Loher, P., Telonis, A. G., Quann, K., Clark, P., Jing, Y., Hatzimichael, E., Kirino, Y., Honda, S., Lally, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420955112 · Cited by 404 · see citing works
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Research works printed but not linked: 1
- Backes,C. et al. (2017) miRCarta: a central repository for collecting miRNA candidates. Nucleic Acids Res., doi: 10.1093/nar/gkx851. · DOI
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A mouse tissue atlas of small noncoding RNA
Isakova, A., Fehlmann, T., Keller, A., & Quake, S. R. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2002277117 · Cited by 119 · see citing works
Self-citationEngel, A., Wagner, V., Hahn, O., Foltz, A. G., Atkins, M., Beganovic, A., Guldner, I. H., Lu, N., Saksena, A., Fischer, U., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59860-6 · Cited by 18 · see citing works
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- Authors
- Fehlmann, T., Backes, C., Alles, J., Fischer, U., Hart, M., Kern, F., Langseth, H., Rounge, T., Umu, S. U., Kahraman, M., Laufer, T., Haas, J., Staehler, C., Ludwig, N., Hübenthal, M., Meder, B., Franke, A., Lenhof, H.-P., Meese, E., & Keller, A.
- Affiliations
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Human Genetics, Saarland University, Homburg, Germany
- Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-21
- Volume
- 34
- Issue
- 10
- Pages
- 1621-1628
- ISSN
- 1367-4803
- 1367-4811
- Cited by
- 26
- References
- 3
- Language
- en
- Funders
- Michael J. Fox Foundation
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