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: sandhuks@iisermohali.ac.in, Ph: 91-172-2293182, 91-9915013645
Received October 5, 2015. Revision received February 23, 2016. Accepted March 2, 2016.
Abstract
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.
Key words
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.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
FREE PDF GRATIS: Genome Biol Evol Sup. Info.
