DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5′–3′ ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation.
Tracing and tracking epiallele families in complex DNA populations / Pezone, Antonio; Tramontano, Alfonso; Scala, Giovanni; Cuomo, Mariella; Riccio, Patrizia; De Nicola, Sergio; Porcellini, Antonio; Chiariotti, Lorenzo; Avvedimento, VITTORIO ENRICO. - In: NAR GENOMICS AND BIOINFORMATICS. - ISSN 2631-9268. - 2:4(2020), pp. 1-10. [10.1093/nargab/lqaa096]
Tracing and tracking epiallele families in complex DNA populations
Antonio Pezone
Primo
Investigation
;Alfonso Tramontano;Giovanni Scala;Mariella Cuomo;Patrizia Riccio;Antonio Porcellini;Lorenzo Chiariotti;vittorio Enrico Avvedimento.
Ultimo
2020
Abstract
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5′–3′ ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation.File | Dimensione | Formato | |
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Tracing and tracking epiallele families in complex DNA populations.pdf
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