Three dimensional organization of genome might have guided the dynamics of gene order evolution in eukaryotes
Meenakshi Bagadia, Arashdeep Singh and Kuljeet Singh Sandhu*
- Author Affiliations
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) – Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali
↵* Author for Correspondence: Kuljeet Singh Sandhu, Assistant Professor and Group Leader, Systems Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) – Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali. E-mail: email@example.com, Ph: 91-172-2293182, 91-9915013645
Received October 5, 2015. Revision received February 23, 2016. Accepted March 2, 2016.
In eukaryotes, genes are non-randomly organized into short gene-dense regions or ‘gene-clusters’ interspersed by long gene-poor regions. How these gene-clusters have evolved is not entirely clear. Gene duplication may not account for all the gene-clusters since the genes in most of the clusters do not exhibit significant sequence similarity. In this study, using genome-wide datasets from budding yeast, fruit-fly and human, we show that: i) long-range evolutionary repositioning of genes strongly associate with their spatial proximity in the nucleus; ii) presence of evolutionary DNA break-points at involved loci hints at their susceptibility to undergo long-range genomic rearrangements; iii) correlated epigenetic and transcriptional states of engaged genes highlight the underlying evolutionary constraints. The significance of observation i, ii & iii are particularly stronger for the instances of inferred evolutionary gain, as compared to loss, of linear gene-clustering. These observations suggest that the long-range genomic rearrangements guided through 3D genome organization might have contributed to the evolution of gene order. We further hypothesize that the evolution of linear gene-clusters in eukaryotic genomes might have been mediated through spatial interactions among distant loci in order to optimize co-ordinated regulation of genes. We model this hypothesis through a heuristic model of gene-order evolution.
Genome organization gene-clusters genomic rearrangements chromatin interactions
© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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