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

Content Provider	Springer Nature : BioMed Central
Author	Lumsden, Amanda L. Ma, Yuefang Ashander, Liam M. Stempel, Andrew J. Keating, Damien J. Smith, Justine R. Appukuttan, Binoy
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.
Related Links	https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/s13104-018-3384-8.pdf
Ending Page	8
Page Count	8
Starting Page	1
File Format	HTM / HTML
ISSN	17560500
DOI	10.1186/s13104-018-3384-8
Journal	BMC Research Notes
Issue Number	1
Volume Number	11
Language	English
Publisher	BioMed Central
Publisher Date	2018-05-09
Access Restriction	Open
Subject Keyword	Biomedicine Medicine Public Health Life Sciences Intercellular adhesion molecule ICAM-1 ICAM-1-related Promoter Medicine/Public Health
Content Type	Text
Resource Type	Article
Subject	Biochemistry, Genetics and Molecular Biology Medicine
Journal Impact Factor	1.6/2023

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