Deciphering long non-coding RNAs
RNA, not just an intermediary between DNA and proteins, is a multifaceted molecule involved in many cellular processes. One particular class of RNA molecules called long non-coding RNAs, or lncRNAs, have long interested researchers. Human cells express thousands of lncRNAs, which resemble their protein-coding cousins (so-called ‘messenger RNAs’) in length and splicing structure, yet they do not serve as templates for protein synthesis.
Researchers in the lab of Eric Lander, founding director of the Broad Institute of MIT and Harvard, have recently turned their attention to a specific lncRNA called NORAD (an acronym derived from “non-coding RNA activated by DNA damage”).
The team describes in Nature how NORAD is essential for assembling a specific protein complex and helps ensure genomic stability.
Using RNA antisense purification and mass spectrometry in a combined method called RAP-MS, the researchers found that NORAD had the strongest binding site for the protein RBMX in human cell lines. They also found that NORAD could control the ability of RBMX to assemble a large protein complex which they termed NARC1 (NORAD-activated ribonucleoprotein complex 1), a finding that hadn’t been previously reported and points towards a novel function of lncRNAs in modulating RNA-binding proteins.
The Broadminded Blog spoke with the study’s lead author Mathias Munschauer, a postdoctoral researcher in the Lander lab, to learn about the significance and scope of lncRNA research.
Why is our understanding of lncRNAs so limited?
Mathias Munschauer: lncRNAs are a relatively recent discovery and were found in large numbers only around 2008 or 2009 when people started to sequence and analyze the complete set of expressed RNAs in cells of various species.
Traditional genes make proteins, therefore most methods to understand gene function focused on proteins. Methods to dissect RNA molecules that do not encode proteins, like lncRNAs, had to be developed. Key techniques started to emerge somewhere between 2013 and 2015.
Other non-coding RNA classes such as microRNAs have a distinct length and bind to specific protein partners, which makes it easier to study their functions and mechanisms. On the contrary, lncRNAs as a group do not bind to common protein complexes. Therefore every lncRNA needs to be dissected on a case-by-case basis, which is a daunting task since there are thousands of lncRNAs in mammalian cells.
What got you interested in studying lncRNAs?
Munschauer: It is fascinating to realize that there are hundreds to thousands of lncRNAs in the genome, but we do not know their purpose. Despite their abundance, geneticists understand the unique functions associated with only a few of them.
Out of the few we know, there is XIST, a lncRNA which can silence the X-chromosome during mammalian female development and TERC, a lncRNA crucial for maintaining specific structures, called telomeres at the end of every chromosome. Both are really intriguing examples. That got me interested in investigating and dissecting the complex biochemical mechanisms of other lncRNAs, such as NORAD.
Why do you think other scientists should pay more attention to lncRNA research?
Munschauer: If researchers want to understand how the genome works, they need to look beyond protein-coding genes and explore regulatory functions of the non-coding genome. The majority of the genome is, in fact, non-coding and the number of non-coding RNAs, including lncRNAs, seems to be close to the number of protein coding mRNAs.
For a long time, lncRNAs were this enigmatic class of RNAs that we did not understand mechanistically, but it became clear relatively soon that at least some of them were functionally important. Now lncRNAs are associated with many diseases including cancer, neurodegenerative diseases, and infectious diseases. Dissecting these lncRNAs mechanistically, may not only reveal new mechanisms of gene regulation but may ultimately also help with the design of RNA-based therapeutics.
Can you give an overview of your recent paper?
Munschauer: We had fairly limited knowledge about the mechanisms by which NORAD maintains genomic stability and wanted to explore that. We thought the most insightful approach would be to look into the proteins that directly bind to this RNA inside a cell.
We found that NORAD binds many nuclear proteins and discovered how it controls the ability of one particular protein to assemble a higher-order complex. Importantly, this complex contains several well-known regulators of genome stability, including topoisomerase I - one of the most important regulators of DNA topology. Now we have a mechanistic understanding of how this particular lncRNA maintains genomic stability because of its ability to form a specific protein complex. This ability of a lncRNA to modulate proteins may not be limited to NORAD alone and other lncRNAs may have similar functions. That will be worth investigating in the future.