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

Kenneth Ramos, Qiang He, Ted Kalbfleisch, Diego E. Montoya-Durango, Ivo Teneng, Vilius Stribinskis, Marcel Brun

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)176-185
Number of pages10
JournalGenomics
Volume90
Issue number2
DOIs
StatePublished - Aug 2007
Externally publishedYes

Fingerprint

Retroelements
Gene Regulatory Networks
Genome
Aryl Hydrocarbon Receptors
RNA Polymerase II
Small Interfering RNA
Drosophila
RNA
Gene Expression
Peptides
DNA

Keywords

  • Aryl hydrocarbon receptor
  • Genetic regulatory networks
  • LINE-1
  • Retrotransposon
  • siRNA knockdown

ASJC Scopus subject areas

  • Genetics

Cite this

Ramos, K., He, Q., Kalbfleisch, T., Montoya-Durango, D. E., Teneng, I., Stribinskis, V., & Brun, M. (2007). Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. Genomics, 90(2), 176-185. https://doi.org/10.1016/j.ygeno.2007.04.003

Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. / Ramos, Kenneth; He, Qiang; Kalbfleisch, Ted; Montoya-Durango, Diego E.; Teneng, Ivo; Stribinskis, Vilius; Brun, Marcel.

In: Genomics, Vol. 90, No. 2, 08.2007, p. 176-185.

Research output: Contribution to journalArticle

Ramos, K, He, Q, Kalbfleisch, T, Montoya-Durango, DE, Teneng, I, Stribinskis, V & Brun, M 2007, 'Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon', Genomics, vol. 90, no. 2, pp. 176-185. https://doi.org/10.1016/j.ygeno.2007.04.003
Ramos, Kenneth ; He, Qiang ; Kalbfleisch, Ted ; Montoya-Durango, Diego E. ; Teneng, Ivo ; Stribinskis, Vilius ; Brun, Marcel. / Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. In: Genomics. 2007 ; Vol. 90, No. 2. pp. 176-185.
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