De Riso, Giulia (2023) MC profiling: a novel approach to dissect DNA methylation heterogeneity in bulk bisulfite sequencing experiments. [Tesi di dottorato]
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| Item Type: | Tesi di dottorato |
|---|---|
| Resource language: | English |
| Title: | MC profiling: a novel approach to dissect DNA methylation heterogeneity in bulk bisulfite sequencing experiments |
| Creators: | Creators Email De Riso, Giulia giulia.deriso@unina.it |
| Date: | 4 March 2023 |
| Number of Pages: | 70 |
| Institution: | Università degli Studi di Napoli Federico II |
| Department: | Medicina Molecolare e Biotecnologie Mediche |
| Dottorato: | Medicina molecolare e biotecnologie mediche |
| Ciclo di dottorato: | 35 |
| Coordinatore del Corso di dottorato: | nome email Santoro, Massimo masantor@unina.it |
| Tutor: | nome email Cocozza, Sergio UNSPECIFIED |
| Date: | 4 March 2023 |
| Number of Pages: | 70 |
| Keywords: | DNA methylation;cellular heterogeneity;epigenetics |
| Settori scientifico-disciplinari del MIUR: | Area 06 - Scienze mediche > MED/03 - Genetica medica |
| Date Deposited: | 21 Mar 2023 10:28 |
| Last Modified: | 10 Apr 2025 14:17 |
| URI: | http://www.fedoa.unina.it/id/eprint/15208 |
Collection description
DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.
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