HOTAIR Long Non-coding RNA: Characterizing the Locus Features by the In Silico Approaches

Abstract

HOTAIR is an lncRNA that has been known to have an oncogenic role in different cancers. There is limited knowledge of genetic and epigenetic elements and their interactions for the gene encoding HOTAIR. Therefore, understanding the molecular mechanism and its regulation remains to be challenging. We used different in silico analyses to find genetic and epigenetic elements of HOTAIR gene to gain insight into its regulation. We reported different regulatory elements including canonical promoters, transcription start sites, CpGIs as well as epigenetic marks that are potentially involved in the regulation of HOTAIR gene expression. We identified repeat sequences and single nucleotide polymorphisms that are located within or next to the CpGIs of HOTAIR. Our analyses may help to find potential interactions between genetic and epigenetic elements of HOTAIR gene in the human tissues and show opportunities and limitations for researches on HOTAIR gene in future studies.

Keywords: CpG Islands; HOTAIR; bioinformatics; epigenetics; gene expression.

Fig. 1

The flowchart of the methods used in the study. TSS, transcription start site; SNP, single nucleotide polymorphism.

Fig. 2

Transcript variants of HOTAIR gene derived from the GENCODE, Ensemble and Refseq.

Fig. 3

Integrated regulatory elements of HOTAIR gene structure. The schematic diagram shows a summary of results from different databases and software which are described in the text.

Fig. 4

CpG Islands in the HOTAIR gene. The data are derived from databases and prediction software. CGI, CpG Island.