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

Genomics & Informatics
Mohammadreza Hajjari, Saghar Rahnama

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.

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Citations

Mar 16, 2019·Frontiers in Genetics·Mohammadreza Hajjari, Saghar Rahnama
Apr 5, 2020·Journal of Translational Medicine·Hossein MozdaraniRoghayeh Rahbar Parvaneh
May 20, 2020·Indian Journal of Hematology & Blood Transfusion : an Official Journal of Indian Society of Hematology and Blood Transfusion·Amira Mohamed Foad ShehataMohamed A Helwa
Mar 17, 2021·Investigative Ophthalmology & Visual Science·Saumik BiswasSubrata Chakrabarti

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Methods Mentioned

BETA
RNA-seq
chip-seq

Software Mentioned

PReMode
MEME
Switchgear
Ensembl
HOTAIR
CpG ProD
MAST
HMM
Repeat Masker
MEME Suite

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