Long non coding RNA are emerging transcriptional species that are increasingly gaining relevance due to their involvement in biological processes. Functionally, lncRNA are known perform regulatory tasks through (i) signal transduction, (ii) sponge formation with microRNA, (iii) protein translocation and guide, (iv) scaffold for molecule assembly and recently (v) triplex formation (Antonov et al. 2019; Hon et al. 2017; Liu et al. 2019).
To achieve functional relevance, lncRNA may either function at the site of transcription (cis) or leave their transcriptional site and effect regulatory roles in distant transcription site (trans) (Latos et al., 2012 ; Rinn et al., 2007) In both cases, they interact with genetic elements to either activate or repress its expression. For example, HOX antisense intergenic RNA HOTAIR, a ~2.2 kb spliced and polyadenylated mammalian transcript that is expressed from the HOXC locus can influence local HOXC expression as well as distant HOXD locus via its repressive activity (Kopp et al., 2018; Rinn et al., 2007).
Deriving the functional significance of multiple lncRNA from experiments remains a bottleneck when prioritizing lncRNA function. Based on the available datasets that have resolved genome wide lncRNA function (in different cells) such as iMARGI, grid-seq and RED-C datasets, genome, we propose a workflow for the functional annotation of lncRNA that accounts for their cis and trans interactions.
The aim of this experiment is to develop and validate a workflow for the functional annotation of lncRNA expression using information from their cis and trans interactions. We would validate these by testing the workflow on lncRNA expression profile from total RNA expression datasets.
Understanding of molecular biology and epigenetics
R, Bash and Python 3.