In recent years, a plethora of novel noncoding RNAs has been identified, yet the vast majority of these transcripts remain poorly characterized. Unlike “traditional” housekeeping noncoding RNAs, such as ribosomal, transfer, or small nuclear RNAs, long noncoding RNAs are expressed at low abundance, which complicates their study of molecular mechanism and necessitates the use of highly sensitive tools.
Next-generation sequencing has emerged as a technology that provides the required sensitivity and resolution to examine the function of low-abundant noncoding RNAs.
The Lee lab studies two viral model systems—Epstein-Barr virus-encoded noncoding RNAs and the RNA genome of Influenza virus—to interrogate RNA-chromatin, RNA-protein, and RNA-RNA interactions. To this end, Lee and colleagues utilize and refine available next-generation sequencing-based techniques for their studies. The advantage of viral systems is that viral components are present in great numbers upon host cell infection by hijacking cellular machineries, thus facilitating their study as well as allowing for optimization of novel RNA-centric techniques. Finally, Lee and his team seek to apply these new RNA tools for the study of novel uncharacterized and low-abundant cellular noncoding RNAs.