ICAM-1-related long non-coding RNA: Promoter analysis and expression in human retinal endothelial cells

Amanda Lumsden, Yuefang Ma, Liam M. Ashander, Andrew J. Stempel, Damien J. Keating, Justine R. Smith, Binoy Appukuttan

Research output: Contribution to journalArticle

Abstract

Objective: Regulation of intercellular adhesion molecule (ICAM)-1 in retinal endothelial cells is a promising druggable target for retinal vascular diseases. The ICAM-1-related (ICR) long non-coding RNA stabilizes ICAM-1 transcript, increasing protein expression. However, studies of ICR involvement in disease have been limited as the promoter is uncharacterized. To address this issue, we undertook a comprehensive in silico analysis of the human ICR gene promoter region. Results: We used genomic evolutionary rate profiling to identify a 115 base pair (bp) sequence within 500 bp upstream of the transcription start site of the annotated human ICR gene that was conserved across 25 eutherian genomes. A second constrained sequence upstream of the orthologous mouse gene (68 bp; conserved across 27 Eutherian genomes including human) was also discovered. Searching these elements identified 33 matrices predictive of binding sites for transcription factors known to be responsive to a broad range of pathological stimuli, including hypoxia, and metabolic and inflammatory proteins. Five phenotype-associated single nucleotide polymorphisms (SNPs) in the immediate vicinity of these elements included four SNPs (i.e. rs2569693, rs281439, rs281440 and rs11575074) predicted to impact binding motifs of transcription factors, and thus the expression of ICR and ICAM-1 genes, with potential to influence disease susceptibility. We verified that human retinal endothelial cells expressed ICR, and observed induction of expression by tumor necrosis factor-α.

Original languageEnglish
Article number285
JournalBMC Research Notes
Volume11
Issue number1
DOIs
Publication statusPublished - 9 May 2018
Externally publishedYes

Keywords

  • ICAM-1
  • ICAM-1-related
  • Intercellular adhesion molecule
  • Promoter

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Lumsden, A., Ma, Y., Ashander, L. M., Stempel, A. J., Keating, D. J., Smith, J. R., & Appukuttan, B. (2018). ICAM-1-related long non-coding RNA: Promoter analysis and expression in human retinal endothelial cells. BMC Research Notes, 11(1), [285]. https://doi.org/10.1186/s13104-018-3384-8