Our research looks at brain function and disease through the lens of mRNA translation. We are particularly interested in alternative modes of translation where ribosomes use unusual/unannotated start or stop codons on mRNAs to generate atypical proteins. Three such modes are shown in Figure 1:
In stop codon readthrough, some of the translating ribosomes continue beyond the stop codon, generating C-terminally extended protein variants.
In upstream and downstream initiation, ribosomes start translation within the 5’UTR or the coding sequence. If in-frame, these events give rise to N-terminally extended or truncated variants. If out-of-frame (not shown in Fig), they generate completely new proteins.
Figure 1. Alternative translation allows a single mRNA to code for multiple protein variants.
By tracking ribosomal positions across mRNAs in the mouse brain, we have identified dozens of transcripts undergoing alternative translation. Building on this discovery, our current research explores the following:
Role of Aquaporin 4 readthrough in neurological diseases
AQP4 is an astrocyte membrane protein and the most abundant water channel in the brain. We have found that Aqp4 transcript undergoes readthrough, and the resulting C-terminally extended AQP4– termed AQP4X— is exclusively localized at astrocyte processes abutting the blood-brain barrier (Figure 2). We have gone on to show that AQP4X enhances the clearance of amyloid beta (the sticky protein that initiates Alzheimer’s disease) from the brain.
In this project, we are continuing to study AQP4X’s role in Alzheimer’s disease. We are also investigating its possible role in ischemic stroke, neuromyelitis optica, and traumatic brain injury in which AQP4 is known to be implicated.
Figure 2. Readthrough-extended AQP4 (AQP4X) is exclusively perivascular. Immunofluorescence staining of the mouse cortex is shown. Note: anti-AQP4 recognizes total (normal plus readthrough) AQP4.
Role of other protein variants in the brain
Besides AQP4X, several other protein variants are in our study list. We are examining two additional readthrough candidates and a few upstream and downstream initiation candidates at this time.
Mechanism of readthrough
Readthrough occurs on a specific set of mRNAs, and not on others, suggesting that it is a regulated phenomenon. Do specific cis elements (features inherent in mRNAs) or trans factors (extrinsic factors such as proteins) modulate readthrough? We are getting interesting answers to this question.
Impact of neurological diseases on alternative translation
Our preliminary data suggest that atypical protein variants and their normal counterparts are differentially impacted in various neurological conditions. This suggests that neurological diseases can impact alternative translation. We are testing this idea by quantifying readthrough, initiation, and translation efficiency (ribosome density over mRNA abundance) in mouse models of neurological conditions.
We use molecular biology, genomics, pharmacology, behavioral science, stereotaxic surgeries, imaging, and mouse genetics in our studies.
Our long-term goal is to illuminate brain function and disease through the standpoint of alternative translation and atypical proteins.
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