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A Mechanistic Study of lncRNA Fendrr Regulation of FoxF1 Lung Cancer Tumor Supressor

  • Carmen NavarroEmail author
  • Carlos Cano
  • Marta Cuadros
  • Antonio Herrera-Merchan
  • Miguel Molina
  • Armando Blanco
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9656)

Abstract

Long non-coding RNAs are known to play multiple roles in the complex machinery of the cell. However, their recent addition to genomic research has increased the complexity of gene expression analyses. In this work, we perform a computational study that aims to contribute to the current understanding of the mechanisms that underlie the experimentally suggested interaction between the lncRNA Fendrr and FoxF1 lung cancer tumor suppressor in carcinogenesis. Results suggest that there exists indeed a multi-level interaction between Fendrr and FoxF1 promoter region, both direct via RNA-DNA:DNA triplex domain formation or mediated by proteins that interact simultaneously with the promoter region of FoxF1 and Fendrr transcripts. Moreover, the applied computational methodology can serve as a pipeline to process any candidate lncRNA-gene pair of interest and obtain putative sources of lncRNA-gene interaction.

Keywords

lncRNAs Gene regulation Computational motif finding Data integration DNA-lncRNA interaction 

Notes

Acknowledgements

This work has been funded as part of projects PI-0710-2013 of J. A., Sevilla and TIN2013-41990-R of DGICT, Madrid and from FEDER. C. Navarro’s work is funded as part of a FPU grant by the Spanish Ministry of Education, Culture and Sports.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Carmen Navarro
    • 1
    Email author
  • Carlos Cano
    • 1
  • Marta Cuadros
    • 2
  • Antonio Herrera-Merchan
    • 3
  • Miguel Molina
    • 4
  • Armando Blanco
    • 1
  1. 1.Department of Computer Science and AIUniversity of GranadaGranadaSpain
  2. 2.Department of Biochemistry and Molecular BiologyUniversity of GranadaGranadaSpain
  3. 3.GENyO, Centre for Genomics and Oncological Research: PfizerUniversity of Granada, Andalusian Regional GovernmentGranadaSpain
  4. 4.Data Science InstituteImperial College LondonLondonUK

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