Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

• DOI: 10.1371/journal.pcbi.1003019
• Publication Date: 2013-03-28T20:59:59Z
• Authors: Marco Di Stefano; Angelo Rosa; Vincenzo Belcastro; Diego di Bernardo; Cristian Micheletti
• Keywords: Colocalization; Chromosome conformation capture

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 their spatial proximity. This fact poses more general question whether it at all feasible numerous are coregulated on a given chromosome, especially those large genomic distances, might become proximate inside nucleus. problem studied here using steered molecular dynamics simulations in order enforce colocalization thousands knowledge-based sequences model for gene-rich human chromosome 19. Remarkably, found most (≈ 88%) pairs can brought simultaneously into contact. made possible low degree intra-chromosome entanglement number cliques coregulatory network. A clique set together as group. constrained conformations 19 further shown organized macrodomains similar inferred from recent HiC measurements. findings indicate largely compatible this relationship exploited draft overall vivo. validity implications these could investigated applying other eukaryotic chromosomes transferable computational strategy introduced here.