LncVar: a database of genetic variation associated with long non-coding genes

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Long non-coding RNAs (lncRNAs) play crucial roles in biological pathways and disease, but their functions are often uncharacterized.
• Genetic variations, such as SNPs and structural variations, are prevalent in lncRNA regions, potentially impacting their function.
• Understanding the effects of these genetic variations is critical given the growing body of lncRNA research.

Purpose of the Study:

• To develop LncVar, a comprehensive database for genetic variations associated with long non-coding genes.
• To systematically analyze the functional impact of genetic variations on lncRNA transcription, modification, and translation.
• To provide a resource for evaluating how genetic variations affect lncRNA biological functions and their roles in disease.

Main Methods:

• Collected lncRNAs from the NONCODE database and assessed their conservation across six species.
• Integrated data on transcription factor binding sites and m6A modification sites for lncRNAs.
• Analyzed the effects of single nucleotide polymorphisms (SNPs) on lncRNA transcription and modification.
• Identified synonymous and non-synonymous SNPs within putatively translated open reading frames (ORFs) of lncRNAs.
• Collected expression quantitative trait loci (eQTLs) for lncRNAs from existing literature.
• Identified lncRNAs in copy number variation (CNV) regions as potential cancer prognostic biomarkers.
• Predicted lncRNA gene fusion events using RNA-seq data from cell lines.

Main Results:

• LncVar provides a systematic evaluation of genetic variation effects on lncRNAs, including impacts on transcription and m6A modification.
• The database includes analysis of SNPs within lncRNA ORFs and associated eQTLs.
• Identified lncRNAs in CNV regions as potential prognostic biomarkers for cancers.
• Predicted lncRNA gene fusion events, offering insights into potential disease mechanisms.
• LncVar serves as a valuable resource for exploring the functional consequences of genetic variations in lncRNAs.

Conclusions:

• LncVar offers a centralized resource for investigating the functional impact of genetic variations on lncRNAs.
• The database aids in understanding the role of lncRNA genetic variations in disease mechanisms and biomarker discovery.
• LncVar facilitates research into the complex interplay between genetic variation and lncRNA function.