title: Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon.
abstract: Computational approaches were used to define structural and functional determinants of a putative genetic regulatory network of murine LINE-1 (long interspersed nuclear element-1), an active mammalian retrotransposon that uses RNA intermediates to populate new sites throughout the genome. Polymerase (RNA) II polypeptide E AI845735 and mouse DNA homologous to Drosophila per fragment M12039 were identified as primary attractors. siRNA knockdown of the aryl hydrocarbon receptor NM_013464 modulated gene expression within the network, including LINE-1, Sgpl1, Sdcbp, and Mgst1. Genes within the network did not exhibit physical proximity and instead were dispersed throughout the genome. The potential impact of individual members of the network on the global dynamical behavior of LINE-1 was examined from a theoretical and empirical framework.
authors.affiliation: Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA. kenneth.ramos@louisville.edu
authors.forename: Kenneth S
authors.initials: KS
authors.lastname: Ramos
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.forename: Ted
authors.initials: T
authors.lastname: Kalbfleisch
authors.forename: Diego E
authors.initials: DE
authors.lastname: Montoya-Durango
authors.forename: Ivo
authors.initials: I
authors.lastname: Teneng
authors.forename: Vilius
authors.initials: V
authors.lastname: Stribinskis
authors.forename: Marcel
authors.initials: M
authors.lastname: Brun
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D053263:Gene Regulatory Networks; D016678:Genome; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D051379:Mice; D008954:Models, Biological; D008957:Models, Genetic; D012313:RNA / Q000378:metabolism; D018336:Receptors, Aryl Hydrocarbon / Q000235:genetics
chemical_list: D018336:Receptors, Aryl Hydrocarbon; D012313:RNA