Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence

Alon Diament, Tamir Tuller

Research output: Contribution to journalArticlepeer-review

Abstract

It has recently been shown that the organization of genes in eukaryotic genomes, and specifically in 3D, is strongly related to gene expression and function and partially conserved between organisms. However, previous studies of 3D genomic organization analyzed each organism independently from others. Here, we propose an approach for unified interorganismal analysis of gene organization based on a network representation of Hi-C data. We define and detect four classes of spatially co-evolving orthologous modules (SCOMs), i.e. gene families that coevolve in their 3D organization, based on patterns of divergence and conservation of distances. We demonstrate our methodology on Hi-C data fromSaccharomyces cerevisiae and Schizosaccharomyces pombe, and identify, among others, modules relating to RNA splicing machinery and chromatin silencing by small RNA which are central to S. pombe's lifestyle. Our results emphasize the importance of 3D genomic organization in eukaryotes and suggest that the evolutionary mechanisms that shape gene organization affect the organism fitness and phenotypes. The proposed algorithms can be utilized in future studies of genome evolution and comparative analysis of spatial genomic organization in different tissues, conditions and single cells.

Original languageEnglish
Pages (from-to)4330-4343
Number of pages14
JournalNucleic acids research
Volume45
Issue number8
DOIs
StatePublished - 5 May 2017

All Science Journal Classification (ASJC) codes

  • Genetics

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