Location, location, location! The package must be labeled properly for delivery!

Picture a large, bustling city with many distinct districts. There’s a government center, a central business district, an industrial center, and maybe a historical or cultural ward. Each of these regions within a city serve a unique and important purpose to the city as a whole and needs specific materials and resources to function. Let’s say that the central business district is growing and needs to build a new skyscraper to provide additional workspaces. To do this, the city works with an architectural firm who mails them blueprints for the building. The blueprints are addressed to the central business district with a specific zip code, and the city’s mail delivery service reads this zip code to successfully deliver the blueprints to the correct location.

Matthew and his team investigate how RNA is moved to the right place inside cells

This is a lot like a process called RNA localization that happens in our cells! If you think of a cell as a city, RNA is like the blueprints that can be sent to different compartments (i.e., “districts”) of the cell, carrying instructions for proteins to be made there. We know that these RNAs have specific “zip codes,” or sequence patterns, that determine the location that they wind up in, with help from specialized RNA-binding proteins, but we don’t yet know what most of these zip codes actually say. That’s the mystery that Dr. Matthew Taliaferro and his research team are trying to solve.

Why is the RNA research that Matthew and his team work on in their lab so important?

The Taliaferro lab’s research findings are far-reaching and have implications for biology as a whole. While RNA localization is a fundamental part of regulating gene expression, in turn impacting what proteins our cells make and where, the field lacks a comprehensive understanding of what RNA sequences and proteins are involved. Dr. Taliaferro and his team want to shed light on this process, enabling discovery of how fundamental biology is linked to mechanisms of disease.  The complex processes that underlie RNA localization have many varied implications for development and disease.

The Taliaferro lab wants to understand these processes better so they can help develop treatments for diseases that happen when these processes go wrong, such as Fragile X Syndrome and amyotrophic lateral sclerosis (ALS).

How does the Taliaferro lab study RNA localization?

Dr. Taliaferro and his team study the localization of RNA in the context of different proteins that bind to RNA to help it figure out where to go inside the cell. These proteins are called RNA-binding proteins. The lab starts with highly scalable neuron-like cell lines from mice that can be induced to grow long, neuron-shaped projections and behave as neurons. They remove their RNA-binding protein of interest from these cells, then they grow the cells with and without the protein. Once the cells have grown into their neuron-like shape, they physically separate the long projections from the cell body (this is called subcellular fractionation) and sequence the RNA from each section. Comparing cells with and without the transport protein allows them to identify RNAs that rely on the specific RNA-binding protein to reach the neuronal projections. From a clinical perspective, these RNAs could contribute to diseases associated with defects in the transport protein, as they are not being properly localized.

In addition to identifying mislocalized RNAs, the Taliaferro lab aims to pinpoint the “zip code” sequences that direct the RNA to a specific cellular location. They do this by systematically testing the ability of thousands of RNA sequences to drive an RNA molecule to a defined place in the cell. By comparing what these successful sequences have in common, they hope to build computer models that can predict whether any given RNA sequence can control this kind of transport. This would help scientists figure out the function of previously unexplained parts of the human genome, and explain why certain mutations lead to disease. Together, these efforts provide insight into the essential biology underlying the regulation of RNA, which has implications for processes as basic as cell division and as complex as diseases with no cure.

What have the Taliaferro lab discovered?

Two RNA-binding proteins that the Taliaferro lab have investigated so far are called FMRP and TDP-43. In recent years, they’ve been able to uncover new and exciting insights into the mechanisms of each of these proteins and how they recognize and bind to RNA.

FMRP is a protein whose deficit causes a disease called Fragile X Syndrome. Symptoms of Fragile X Syndrome commonly include delays in development, learning disabilities, and social and behavioral problems. FMRP has been known to function widely in RNA localization and in the control of RNA production. However, the RNAs that depend on FMRP for transport were unknown. Using the sequencing and motif-identification discussed above, the Taliaferro lab found that there’s a specific shape of RNA (called a G-quadraplex), formed by sequences of RNA that are rich in the RNA base guanine (G), that FMRP recognizes as a signal to bind for RNA transport. This finding could directly help to guide future studies of Fragile X Syndrome, potentially shedding light on mechanisms underlying this complex disorder. This discovery also broadly suggests a framework for how additional RNA-binding proteins might identify their targets to transport RNA.

TDP-43 is a protein known to contribute to the development of ALS, a fatal disease that initially causes muscle weakness and eventually progresses into complete loss of mobility. Previously, TDP-43 has been shown to help control the localization of RNA in neurons. However, with the use of subcellular fractionation and specific sequencing, the Taliaferro lab determined that, rather than promoting RNA localization to the projections of neurons, TDP-43 is actually promoting the breakdown of the RNAs that it interacts with, preventing them from being transported. This surprising finding informs future studies of RNA-binding and transport and will potentially influence our understanding of how ALS develops.  

What the clinical implications of this research?

The improper localization of RNAs in a cell can have cascading downstream effects that cause system-level developmental defects or disease. Every RNA “zip code” that the Taliaferro lab cracks is one step closer to understanding some of the most complex human diseases. Knowledge of where and when an RNA is being used by the cell (as we can determine from its “zip code”) is equally important to understanding the identity of the RNA itself. When RNA doesn’t wind up where it is supposed to, the protein it encodes can be similarly mislocalized, stopping it from properly functioning. RNA that ends up in the wrong place in the cell (RNA mislocalization) can also result in disruption to the precise balance of protein complexes, which could shut down relevant, essential signaling pathways. In sum, when correctly built proteins don’t show up in the right place at the right time, the consequences could lead to lifelong and/or fatal disease, such as Fragile X Syndrome or ALS.

What are the future directions for the research?

The research in the Taliaferro lab highlights that studying RNA can reveal new insight into fundamental biology and guide how we might better diagnose and treat RNA-associated human diseases.

If you want to learn more about the scientist, please head to their official CU webpage