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Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data


Autoři: Nazifa Ahmed Moumi aff001;  Badhan Das aff001;  Zarin Tasnim Promi aff001;  Nishat Anjum Bristy aff001;  Md. Shamsuzzoha Bayzid aff001
Působiště autorů: Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh aff001
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0221270

Souhrn

Understanding cell differentiation—the process of generation of distinct cell-types—plays a pivotal role in developmental and evolutionary biology. Transcriptomic information and epigenetic marks are useful to elucidate hierarchical developmental relationships among cell-types. Standard phylogenetic approaches such as maximum parsimony, maximum likelihood and neighbor joining have previously been applied to ChIP-Seq histone modification data to infer cell-type trees, showing how diverse types of cells are related. In this study, we demonstrate the applicability and suitability of quartet-based phylogenetic tree estimation techniques for constructing cell-type trees. We propose two quartet-based pipelines for constructing cell phylogeny. Our methods were assessed for their validity in inferring hierarchical differentiation processes of various cell-types in H3K4me3, H3K27me3, H3K36me3, and H3K27ac histone mark data. We also propose a robust metric for evaluating cell-type trees.

Klíčová slova:

Blood – Cell differentiation – Epigenetics – Fibroblasts – Lung development – Phylogenetic analysis – Phylogenetics – principal component analysis


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