Tobias Fehlmann1, Christina Backes1, Julia Alles2, Ulrike Fischer2, Martin Hart2, Fabian Kern1, Hilde Langseth3, Trine Rounge3, Sinan Ugur Umu3, Mustafa Kahraman1,4, Thomas Laufer4, Jan Haas5,6,7, Cord Staehler1, Nicole Ludwig2, Matthias Hübenthal8, Benjamin Meder5,6,7, Andre Franke8, Hans-Peter Lenhof9, Eckart Meese2, Andreas Keller1. 1. Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany. 2. Department of Human Genetics, Saarland University, 66421 Homburg, Germany. 3. Cancer Registry of Norway, Institute of Population-based Cancer Research, N-0304 Oslo, Norway. 4. Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany. 5. Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany. 6. German Center for Cardiovascular Research (DZHK), 69120 Heidelberg, Germany. 7. Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany. 8. Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany. 9. Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
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. Contact: c.backes@mx.uni-saarland.de or andreas.keller@ccb.uni-saarland.de. Supplementary information: Supplementary data are available at Bioinformatics online.
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. Contact: c.backes@mx.uni-saarland.de or andreas.keller@ccb.uni-saarland.de. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Julia Alles; Tobias Fehlmann; Ulrike Fischer; Christina Backes; Valentina Galata; Marie Minet; Martin Hart; Masood Abu-Halima; Friedrich A Grässer; Hans-Peter Lenhof; Andreas Keller; Eckart Meese Journal: Nucleic Acids Res Date: 2019-04-23 Impact factor: 16.971
Authors: Sinan Uğur Umu; Hilde Langseth; Andreas Keller; Eckart Meese; Åslaug Helland; Robert Lyle; Trine B Rounge Journal: Mol Oncol Date: 2020-01-10 Impact factor: 6.603
Authors: Tobias Fehlmann; Benoit Lehallier; Nicholas Schaum; Oliver Hahn; Mustafa Kahraman; Yongping Li; Nadja Grammes; Lars Geffers; Christina Backes; Rudi Balling; Fabian Kern; Rejko Krüger; Frank Lammert; Nicole Ludwig; Benjamin Meder; Bastian Fromm; Walter Maetzler; Daniela Berg; Kathrin Brockmann; Christian Deuschle; Anna-Katharina von Thaler; Gerhard W Eschweiler; Sofiya Milman; Nir Barziliai; Matthias Reichert; Tony Wyss-Coray; Eckart Meese; Andreas Keller Journal: Nat Commun Date: 2020-11-24 Impact factor: 14.919