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Genomics. 2007 Aug;90(2):176-85. Epub 2007 May 22.

Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon.

Author information

1
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

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.

PMID:
17521869
PMCID:
PMC2065750
DOI:
10.1016/j.ygeno.2007.04.003
[Indexed for MEDLINE]
Free PMC Article

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