Research SummaryStructure, functions and recognition of long non-coding (lnc) RNA
Long noncoding RNAs (lncRNAs) are large and diverse class of RNA molecules with > 200 nucleotides length that lack protein coding potential. LncRNAs have gained widespread attention in recent years due to their immense potential to regulate diverse biological processes. Long Intergenic Non-coding RNAs (lincRNAs) are the largest class of lncRNAs in the eukaryotic genome, which originate from the intergenic regions. Although more than 3,000 human lincRNAs have been discovered using transcriptomic data and bioinformatics analysis, only a subset (less than 1%) have been functionally and mechanistically characterized in detail. These RNAs seems to be evolutionarily conserved at least in the mammalian genomes. One of the next challenges in biology is to ascertain the functions and mode of action of the newly discovered lncRNAs.
Here, I proposed to study the structural and mechanistic basis of select lncRNAs involved in gene regulation and telomere maintenance (e.g. TERRA, HOTAIR, lincRNA-p21 etc.). I aim to carryout a detailed phylogenetic, sequence conservation, secondary structure mapping, and recognition by effector proteins of lncRNAs using chemical and enzymatic probing, structural, and computational/bioinformatics approaches. This, I believe will be a timely study and the principles learned will be applicable on other lncRNA-protein systems.
Figure Legend: The sequences of lncRNAs will be analyzed for their conservation, secondary/tertiary structure, and protein binding using chemical and enzymatic probing methods as well as computational/bioinformatics approaches.