Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19

Abstract

The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity. This fact poses the more general question of whether it is at all feasible that the numerous genes that are coregulated on a given chromosome, especially those at large genomic distances, might become proximate inside the nucleus. This problem is studied here using steered molecular dynamics simulations in order to enforce the colocalization of thousands of knowledge-based gene sequences on a model for the gene-rich human chromosome 19. Remarkably, it is found that most (~80%) gene pairs can be brought simultaneously into contact. This is made possible by the low degree of intra-chromosome entanglement and the large number of cliques in the gene coregulatory network, that is the many groups of genes that are all mutually coregulated. The constrained conformations for the model chromosome 19 are further shown to be organised in spatial macrodomains that are similar to those inferred from recent HiC measurements. The findings indicate that gene coregulation and colocalization are largely compatible and that this relationship can be exploited to draft the overall spatial organization of the chromosome in vivo. The more general validity and implications of these findings could be investigated by applying to other eukaryotic chromosomes the general and transferable computational strategy introduced here.

24 pages, 11 figures, Accepted for publication in PLoS Computational Biology

References in corpus (3)

• PLUMED: a portable plugin for free-energy calculations with molecular dynamics
• Mean clustering coefficients: the role of isolated nodes and leafs on clustering measures for small-world networks
• Spatial and topological organization of DNA chains induced by gene co-localization

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