Inside every cell is a bustling metropolis. Emerging from the central hub of the nucleus, ribbons of mRNA transcripts spool into the cytoplasmic suburbs ready to be translated into proteins.
“People think cytoplasm is a bag and it doesn't matter where you go because it's all translated there,” said Christine Mayr, a cell biologist at Memorial Sloan Kettering Cancer Center. “What we saw is, first of all, it's not random where the RNA goes, but then it actually matters.”
Understanding mRNA location and its role in the cytoplasm
In a new study, Mayr and her team reported that the cytoplasm is divided into distinct, membraneless compartments, and that where mRNA translation takes place determines both the amount and the function of the resulting protein (1). The discovery may inform the development of new RNA therapies in the future.
Distinct cellular compartments and targeted mRNA localization
Translation occurs on ribosomes in the cytosol or on the endoplasmic reticulum (ER), but in 2018, Mayr and her colleagues discovered that translation of certain mRNA molecules also occurs in a membraneless structure in the cytoplasm called TIS granules (2). TIS granules form a mesh-like structure that wraps around, but remains distinct from, the ER, and they help the proteins translated within them form complexes.
To determine the identities of the transcripts translated in TIS granules as well as on the ER and the cytosol, Mayr and her team isolated the three different structures and performed RNA sequencing on their contents. Much to their surprise, the transcripts enriched at each site had distinct characteristics.
“First, of course, I thought my student did something wrong,” Mayr laughed. “But she repeated it 100 times or something like that, and we always got the same thing.”
People think cytoplasm is a bag and it doesn't matter where you go because it's all translated there. What we saw is, first of all, it's not random where the RNA goes, but then it actually matters.
- Christine Mayr, Memorial Sloan Kettering Cancer Center
Transcripts encoding small proteins traveled to the cytosol; low abundance protein transcripts and those encoding transcription factors went to TIS granules; and large and highly expressed ones headed to the ER.
How the cell dictates mRNA location
Mayr and her team hypothesized that RNA binding proteins shuttled the mRNA transcripts to different compartments, but when they deleted RNA binding proteins and watched where the transcripts went, they realized that mRNA length, exon length, and number of exons in a particular transcript formed a combinatorial code with different RNA binding proteins that determined where a transcript ended up.
“All these architecture features, they actually really play a primary role in this,” she said. “I find that quite beautiful.”
The impact of mRNA location on protein expression and function
Most surprising, Mayr added, was that redirecting an mRNA to a different location dramatically changed how much of the protein was made and the kinds of protein complexes it formed. When they sent a transcript normally translated in the cytosol to the ER instead, it had a 3.5-fold increase in its protein expression. In a parallel project, the researchers redirected the translation of the cancer oncogene MYC away from its normal location in the TIS granules to the cytosol (3). When translated in the TIS granules, MYC forms protein complexes that regulate MYC target gene expression in the nucleus, but when translated in the cytosol, these complexes do not form, thereby altering MYC’s protein function.
The ability to change a protein’s expression level and function based on where in the cell its translation occurs has exciting implications for RNA and protein drug development.
“My hope is really that in the future, you can make much smarter proteins,” said Mayr. “If it's translated in the cytosol, [it] has function number one. If it's translated in the granule, then it forms a complex, has function number two. You could basically design it like that.”
Frequently asked questions about mRNA location
Where is mRNA located after it leaves the nucleus?
After being transcribed in the nucleus, mRNA travels out into the cytoplasm, where it can be found in different compartments, including the cytosol, on the endoplasmic reticulum (ER), and in specialized membraneless structures like TIS granules. The specific mRNA location is not random.
What determines where an mRNA molecule is located within the cytoplasm?
The location of an mRNA molecule is determined by a "combinatorial code" that involves the mRNA's architectural features—such as its length, exon length, and number of exons—working together with specific RNA binding proteins that act as shuttles.
Why does a specific mRNA location matter for protein synthesis?
A recent study showed that the specific location of an mRNA transcript determines both the amount of protein produced and the function of the resulting protein. Redirecting an mRNA to a different location can dramatically change the outcome of its translation.
What are TIS granules, and what is their role?
TIS granules are specialized, membraneless compartments in the cytoplasm where certain mRNA molecules are translated. These structures help the proteins formed within them to properly assemble into functional complexes.
References
- Horste, E.L. et al.Subcytoplasmic location of translation controls protein output. Mol Cell 83, 4509-4523.e11 (2023).
- Ma, W. and Mayr, C. A Membraneless Organelle Associated with the Endoplasmic Reticulum Enables 3′UTR-Mediated Protein-Protein Interactions. Cell 175, 1492-1506.E19 (2018).
- Luo, Y. et al. mRNA interactions with disordered regions control protein activity. Preprint at: https://www.biorxiv.org/content/10.1101/2023.02.18.529068v1
