KTCNlncDB-a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas

Abstract

Keratoconus (KTCN, OMIM 148300) is a degenerative eye disorder characterized by progressive stromal thinning that leads to a conical shape of the cornea, resulting in optical aberrations and even loss of visual function. The biochemical background of the disease is poorly understood, which motivated us to perform RNA-Seq experiment, aimed at better characterizing the KTCN transcriptome and identification of long non-coding RNAs (lncRNAs) that might be involved in KTCN etiology. The in silico functional studies based on predicted lncRNA:RNA base-pairings led us to recognition of a number of lncRNAs possibly regulating genes with known or plausible links to KTCN. The lncRNA sequences and data regarding their predicted functions in controlling the RNA processing and stability are available for browse, search and download in KTCNlncDB (http://rhesus.amu.edu.pl/KTCNlncDB/), the first online platform devoted to KTCN transcriptome.Database URL: http://rhesus.amu.edu.pl/KTCNlncDB/.

Figure 1.

Possible roles of lncRNAs played in the context of RNA-RNA interactions. (a) Modulating alternative splicing events through masking splice sites and other splicing signals (b) Abrogation of miRNA functions by blocking miRNA target sites; (c) Triggering RNA editing by creating dsRNA substrates for ADAR enzymes (d) Guiding protein-coding transcripts to degradation in a SMD pathway. Provided are examples of lncRNAs and differentially expressed genes predicted to be under their control. The genes belong to TGF-β, Hippo and Wnt-related signaling pathways and they all are downregulated in KTCN (marked with down arrows).