Investigating the link between NAD metabolism and NAD-capped RNAs
RNA regulation operates across multiple interconnected layers, including transcription, RNA processing, chemical modification, translation, and decay. While canonical m⁷G capping and internal RNA modifications such as m⁶A have been extensively characterized, recent discoveries have revealed an addit...
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| Natura: | Book/Monograph Tesi |
| Lingua: | inglese |
| Pubblicazione: |
Heidelberg
29 Jul. 2026
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| DOI: | 10.11588/heidok.00039136 |
| Soggetti: | |
| Accesso online: | Resolving-System, kostenfrei: https://nbn-resolving.org/urn:nbn:de:bsz:16-heidok-391365 Resolving-System, kostenfrei: https://doi.org/10.11588/heidok.00039136 Verlag, kostenfrei, Volltext: http://www.ub.uni-heidelberg.de/archiv/39136 Langzeitarchivierung Nationalbibliothek, kostenfrei: https://d-nb.info/1414870213/34 
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| Note sull'autore: | vorgelegt von Tae Wha Seong, M.Sc. ; supervisors: Prof. Dr. Andres Jäschke [und ein weiterer Gutachter] |
| Riassunto: | RNA regulation operates across multiple interconnected layers, including transcription, RNA processing, chemical modification, translation, and decay. While canonical m⁷G capping and internal RNA modifications such as m⁶A have been extensively characterized, recent discoveries have revealed an additional layer of chemical diversity at RNA 5′ ends. Among these, metabolite-derived caps such as nicotinamide adenine dinucleotide (NAD⁺) represent a non-canonical class of RNA modifications that are incorporated during transcription initiation and directly connect RNA identity to cellular metabolism. Although NAD-capped RNAs have been identified in bacteria and eukaryotes and linked to altered RNA stability and translation, their dynamic regulation and integration with metabolic and chromatin-based regulatory mechanisms remain poorly understood. This thesis systematically investigates NAD-capped RNAs as a metabolically responsive layer of gene regulation across bacterial and human systems. To enable sensitive and quantitative analysis, a novel sequencing framework, HELIOS NAD-Seq, was developed and applied. HELIOS incorporates internal standards, early multiplexing, and calibrated normalization strategies to enhance sensitivity, reduce input requirements, and enable high-throughput, time-resolved analysis of NAD-capping dynamics. Using HELIOS NAD-Seq, NAD-capping landscapes were characterized across defined biological contexts, including E. coli growth phase transitions and metabolic or oxidative stress in human HEK293T cells. The results demonstrate that NAD capping is highly dynamic and acutely sensitive to metabolic perturbation. However, NAD capping does not simply reflect total intracellular NAD abundance or steady-state RNA expression levels. Instead, NAD capping is largely decoupled from transcript abundance and responds to metabolic and redox state in a temporally regulated manner. Time-resolved analyses further revealed a separation between changes in NAD metabolism, global PARP activity, and NAD-capping dynamics, indicating that NAD capping reflects integrative downstream processes rather than immediate fluctuations in NAD availability. Integration of NAD-capping profiles with chromatin accessibility (ATAC-seq), transcription-associated DNA dynamics (KAS-seq), and PARP1 occupancy uncovered locus-specific determinants of NAD-cap incorporation. NAD-capped transcription start sites preferentially localize to accessible, transcriptionally active chromatin regions enriched for promoter-proximal PARP1 binding. These findings support a model in which NAD capping is influenced by chromatin context and local enzymatic environment rather than by global metabolic state alone. Notably, mitochondrial transcripts were recurrently enriched among NAD-capped RNAs, suggesting that mitochondrial transcription and redox balance represent important contexts for NAD-cap formation. Collectively, this work establishes NAD capping as a conserved, metabolically responsive, and locus-specific RNA modification that integrates metabolic state, transcription initiation, and chromatin architecture. By combining experimental innovation with quantitative analysis, this thesis advances the conceptual understanding of NAD capping and lays the groundwork for future studies addressing its functional consequences in cellular adaptation, mitochondrial biology, and metabolic disease. |
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| Descrizione fisica: | Online Resource |
| DOI: | 10.11588/heidok.00039136 |