| Autor: |
Benjamin E. Decato, Jianghan Qu, Xiaojing Ji, Elvin Wagenblast, Simon R. V. Knott, Gregory J. Hannon, Andrew D. Smith |
| Jazyk: |
angličtina |
| Rok vydání: |
2020 |
| Předmět: |
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| Zdroj: |
Epigenetics & Chromatin, Vol 13, Iss 1, Pp 1-14 (2020) |
| Druh dokumentu: |
article |
| ISSN: |
1756-8935 |
| DOI: |
10.1186/s13072-020-00363-7 |
| Popis: |
Abstract Background Partially methylated domains (PMDs) are a hallmark of epigenomes in reproducible and specific biological contexts, including cancer cells, the placenta, and cultured cell lines. Existing methods for deciding whether PMDs exist in a sample, as well as their identification, are few, often tailored to specific biological questions, and require high coverage samples for accurate identification. Results In this study, we outline a set of axioms that take a step towards a functional definition for PMDs, describe an improved method for comparable PMD detection across samples with substantially differing sequencing depths, and refine the decision criteria for whether a sample contains PMDs using a data-driven approach. Applying our method to 267 methylomes from 7 species, we corroborated recent results regarding the general association between replication timing and PMD state, and report identification of several reproducibly “escapee” genes within late-replicating domains that escape the reduced expression and hypomethylation of their immediate genomic neighborhood. We also explored the discordant PMD state of orthologous genes between human and mouse, and observed a directional association of PMD state with gene expression and local gene density. Conclusions Our improved method makes low sequencing depth, population-level studies of PMD variation possible and our results further refine the model of PMD formation as one where sequence context and regional epigenomic features both play a role in gradual genome-wide hypomethylation. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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