Decoding Epigenetic and Epitranscriptomic Regulation with Hypermodified Nucleoside Analogs: Carbocyclic 5-Aza-2’-Deoxycitidine and Allyl- or Homoallyl- DeoxyQueuine

Zitation: Peev, Elsa und Carell, Thomas und Müller, Markus: Decoding Epigenetic and Epitranscriptomic Regulation with Hypermodified Nucleoside Analogs: Carbocyclic 5-Aza-2’-Deoxycitidine and Allyl- or Homoallyl- DeoxyQueuine. 16. März 2026. Open Data LMU. 10.5282/ubm/data.798

Be­schrei­bung

On the subject of queuosine analogus, my students and I took part in a project aimed at determining the role of mannose and galactose additions on queuosine on tRNA. Queuosine is a hypermodified nucleoside that, in vertebrates, is further modified by the recently discovered QTMAN and QTGAL enzymes. The role of the addition of those extra-moieties is not fully understood. With the development of queuosine analogues, we were able to separate the two sugars in distinct cell samples and evaluate their roles independently. The results show that, with our strategy, we maintain the known role of mannose in biological functions such as growth and development. As innovation, we were able to link galactose to immunological functions and support for mitochondrial matrix balance. The latter role is linked to the prevention of neurodegenerative diseases such as Parkinson's and Alzheimer's. READ ME note in the folder(s) contains all the meaningful informations: Disclaim regarding “Proteomic data and enrichment for the Q-Project” · The data here are serval set that represent the different analysis and steps as describe in the PhD thesis of Elsa Peev (Decoding Epigenetic and Epitranscriptomic Regulation with Hypermodified Nucleoside Analogs: Carbocyclic 5-Aza-2’-Deoxycitidine and Allyl- or Homoallyl- DeoxyQueuine) that lead to the output as presented into my thesis with the analysis as describe into the method Each Set contains a "READ ME" note specific to each analysis and data display. Brief description of the project associate: The extensive proteomic data generate here are part of the a project to decode the specific role of Mannosyl-Queuosine and Galactosyl-Queuosine. We used the chemical biology tools our laboratory have created and published in 2025 (https://doi.org/10.1002/anie.202508499) to be able to analyse the role of those modified Q separately. After systematic approach to prove selectivity and specificity of our probes (see paper), we used them to see the biological path that are dependant of those modification and map their specificity. Our unique time-frame analysis allowed to view all the biological process that are known to depend on Queuosine, ManQ and GalQ all together but our innovation lead to sort and classify the biological functions according to the presence or absence of the additional glycosylation event. Briefly, cells were fed with 20 µM of queuine (q) or queuine analogues (3dq [GalQ], 2dq [ManQ]) or DMSO control and harvested at different time point. All samples are from HEK293T protein extract and process according to the SP3 protocol (https://doi.org/10.15252/msb.20145625). · /!\ Possible Nomenclature Mistake /!\: All data set name should have been correct to fit the names displayed into the published results (F, q, 3dq,2dq, etc.), however mistakes can be hidden. In this case, the pre-published nomenclature may be present in certain file, if I missed to corrected it, here is the meaning: N = F = Full Q = q = queuine-fed Q13 = 2dq = 2-deoxyqueuine-fed Q12 = 3dq = 3-deoxyqueuine-fed D = DMSO = DMSO Control · All protein recorded are in the excel file "0_QProject-RawProteomicSet" · Following folder are downstream processed data, they were organized by time point as presented in the thesis and also, not presented in the thesis, by compounds. What it means: Per compound means (folder name "SortedByCompound"): At each time, the samples are compared to each other. No protein was significative enriched in most of this set but there is serval that are present only in 1 sample. Per Time point means (folder name "SortedByTimeFrame"): All data for each compound is analyzed as comparison of them self through time. For example: q-fed samples are harvested at time point 0, 24, 48 and 120 hours. Overall proteome at each time point of each compound is analyzed as the comparison of it own evolution through time ("0h_q vs. 24h_q", "0h_q vs. 48h_q", etc.). The resulting protein set are filtered by first, grouping the protein that are up or down regulated and then keeping the protein that are exclusively present in 1 sample of the compared set and the protein that are significantly enriched (p-value <0.05). The filtered data set are all loaded in metascape. Only for the "Per Time Point” ! Metascape Outputs (folder "GO-KEGG_Enrichement") The enrichment was done on the three GO Terms: Molecular Function (MF), Biological Process (BP), Cellular Component (CC) and for the KEGG Pathways. The Overall Out-Put is in the sub-folder: "First-Metascape-OutPut_RowData" The biological process outputs were further sorted and analyzed through their parental go terms (File "GO_MCODE" in each "Enrichement_PPI" File for each analysis) and Output is in the file "BP-SortedData_PerParentalGoTerms"

Stichwörter

Queuine, 2-deoxy-queuine, 3-deoxy-queuine, Mannosyl-Queuosine, Galactosyl-Queuosine, proteomic, proliferation, growth, development, immunology, homeostasis

• Dokumententyp: Daten
• Name der Kontakt­person: Peev, Elsa
• E-Mail der Kontaktperson: elsapeev at gmail.com
• Fächer: Chemie und Pharmazie
• Dewey Dezimal­klassi­fikation: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 540 Chemie
• Eingestellt von: Ms Elsa Peev