Low Depth Epigenetic Mapping of Maturation Versus Retrodifferentiation in HepaRG Cells
Abstract
Background: Long-read, single-CpG-resolution sequencing is redefining the information-to-depth ratio in epigenomics. While conventional methylome analysis often requires high coverage, we propose a scalable pipeline designed to extract high-density regulatory logic from shallow sequencing data. Methods: By utilizing the progenitor-like HepaRG cell line as a model for liver plasticity, we validated this framework across two divergent developmental trajectories: hepatic maturation and sphere-induced retrodifferentiation. Our technical approach combines CpG-centric enrichment and regional methylation aggregation to reconstruct regulatory landscapes from sparse data. Using long-read Nanopore sequencing, we mapped the dynamics of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Results: Our pipeline revealed that these trajectories are not inverse processes but engage distinct epigenetic strategies. Hepatic maturation is characterized by the accumulation of 5hmC that partially targets repressive heterochromatin (H3K9me3, H4K20me3) and pioneer factors such as FOXA2. In contrast, retrodifferentiation increases 5mC, potentially silencing adult regulators such as HNF1A via Polycomb-associated networks. In addition, aggregation-based analysis can distinguish widespread focal perturbations from a restricted subset of transcription factors that translate epigenetic changes into regional accessibility. Conclusions: This study provides a scalable computational framework for investigating cellular fate transitions, proving that high-value epigenetic insights are attainable even at reduced sequencing depths.
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BibTeX
@article{hernandezvargas2026depth,
title = {{Low Depth Epigenetic Mapping of Maturation Versus Retrodifferentiation in HepaRG Cells}},
author = {Hector Hernandez-Vargas and Kilian Petitjean and Marie-Pierre Lambert and Yoann Daniel and Isabelle Chemin and Anne Corlu and Chloe Goldsmith},
journal = {Epigenomes},
year = {2026},
month = oct,
doi = {10.3390/epigenomes10020036},
url = {https://hal.science/hal-05683512v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Low Depth Epigenetic Mapping of Maturation Versus Retrodifferentiation in HepaRG Cells
AU - Hector Hernandez-Vargas
AU - Kilian Petitjean
AU - Marie-Pierre Lambert
AU - Yoann Daniel
AU - Isabelle Chemin
AU - Anne Corlu
AU - Chloe Goldsmith
PY - 2026
DA - 2026/10/16
JO - Epigenomes
DO - 10.3390/epigenomes10020036
UR - https://hal.science/hal-05683512v1
AB - Background: Long-read, single-CpG-resolution sequencing is redefining the information-to-depth ratio in epigenomics. While conventional methylome analysis often requires high coverage, we propose a scalable pipeline designed to extract high-density regulatory logic from shallow sequencing data. Methods: By utilizing the progenitor-like HepaRG cell line as a model for liver plasticity, we validated this framework across two divergent developmental trajectories: hepatic maturation and sphere-induced retrodifferentiation. Our technical approach combines CpG-centric enrichment and regional methylation aggregation to reconstruct regulatory landscapes from sparse data. Using long-read Nanopore sequencing, we mapped the dynamics of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Results: Our pipeline revealed that these trajectories are not inverse processes but engage distinct epigenetic strategies. Hepatic maturation is characterized by the accumulation of 5hmC that partially targets repressive heterochromatin (H3K9me3, H4K20me3) and pioneer factors such as FOXA2. In contrast, retrodifferentiation increases 5mC, potentially silencing adult regulators such as HNF1A via Polycomb-associated networks. In addition, aggregation-based analysis can distinguish widespread focal perturbations from a restricted subset of transcription factors that translate epigenetic changes into regional accessibility. Conclusions: This study provides a scalable computational framework for investigating cellular fate transitions, proving that high-value epigenetic insights are attainable even at reduced sequencing depths.
SN - 2075-4655
ER -