High-throughput technology for detection of RNA modifications
Final Report Abstract
RNA modifications are chemical alterations of the four classical nucleosides typically contained in naturally occurring RNA. Recent progress has unveiled a strong influence on such modifications on a plethora of aspects of the regulation of gene expression, even including aspects of inheritance. The latter being unrelated to the sequence information of the genome proper has led to the coining of epitranscriptomics as a key word that now characterizes the field. Progress in this field is strongly limited by the lack of methods suited to accurately and precisely determine the positions of the up to 150 chemically distinct RNA modifications in the sequence of the epitranscriptome. In the course of this project, several types of chemistry were tested for their suitability to be used in approaches of RNA high-throughput sequencing (RNA seq). For two types of RNA modifications, namely m1A and Nm, methods were developed to the level of fully-fledged analysis packages including bioinformatic tools for screening a given transcriptome.
Publications
- (2015) The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent.Nucleic Acids Research, Sep. 13, 43(20):9950-64
Hauenschild, R., Tserovski, L., Schmid, K., Thüring, K., Winz, ML., Sharma, S., Entian, KD., Wacheul, L., Lafontaine, DL., Anderson, J., Alfonzo, J., Hildebrandt, A., Jäschke, A., Motorin, Y., Helm, M.
(See online at https://doi.org/10.1093/nar/gkv895) - CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles, (2016) Biomolecues., Nov. 10, 6(4)
Hauenschild, R., Werner, S., Tserovski, L., Hildebrandt, A., Motorin, Y., Helm, M.
(See online at https://doi.org/10.3390/biom6040042) - Diastereoselectivity of 5-methyluridine osmylation is inverted inside an RNA chain., (2016) Bioconjugate Chemistry, Aug. 19, 27(9):2188-97
Tserovski, L., Helm, M.
(See online at https://doi.org/10.1021/acs.bioconjchem.6b00403) - Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA., (2016) Nucleic Acid Research, Jun. 14, 44(16):e135
Marchand, V., Blanloeil- Oillo, F., Helm, M., Motorin, Y.
(See online at https://doi.org/10.1093/nar/gkw547) - Alkyne-Functionalized Coumarin Compound for Analytic and Preparative 4-Thiouridine Labeling, (2017), Bioconjugate Chemistry, Mar. 15, 28(4):1123-1134
Schmid, K., Adobes-Vidal, M., Helm, M.
(See online at https://doi.org/10.1021/acs.bioconjchem.7b00035) - Detecting RNA modifications in the epitranscriptome: predict and validate, (2017), Nature Reviews Genetics, Feb. 20
Helm, M., Motorin, Y.
(See online at https://doi.org/10.1038/nrg.2016.169) - Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation, (2017), Biomolecules, Feb. 9, 7(1)
Marchand, V., Pichot, F., Thüring, K., Avadi, L., Freund, I., Dalpke, A., Helm, M., Motorin, Y.
(See online at https://doi.org/10.3390/biom7010013) - Engineering of a DNA polymerase for direct m6A Sequencing, (2018), Angew. Chem. Int. Ed. Engl., Jan. 8, 57,417-421
Aschenbrenner, J., Werner, S., Marchand, V., Adam, M., Motorin , Y., Helm, M., Marx, A.
(See online at https://doi.org/10.1002/anie.201710209)
