2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2020

Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Syst, 8(6):494-505. 2019. Also at https://www.biorxiv.org/content/10.1101/552505v1.full-text.

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Recent whole-genome mapping approaches for the chromatin interactome have offered
new insights into 3D genome organization. However, our knowledge of the
evolutionary patterns of 3D genome in mammals remains limited. In particular,
there are no existing phylogenetic-model-based methods to analyze chromatin
interactions as continuous features. Here, we develop phylogenetic hidden Markov 
random field (Phylo-HMRF) to identify evolutionary patterns of 3D genome based on
multi-species Hi-C data by jointly utilizing spatial constraints among genomic
loci and continuous-trait evolutionary models. We used Phylo-HMRF to uncover
cross-species 3D genome patterns based on Hi-C data from the same cell type in
four primate species (human, chimpanzee, bonobo, and gorilla). The identified
evolutionary patterns of 3D genome correlate with features of genome structure
and function. This work provides a new framework to analyze multi-species
continuous genomic features with spatial constraints and has the potential to
help reveal the evolutionary principles of 3D genome organization.