XU LABORATORY
INSTITUTE FOR CELL ENGINEERING
DEPARTMENT OF NEUROLOGY | JOHNS HOPKINS SCHOOL OF MEDICINE
Brain Resilience
Translation is dynamic
Over the course of development or over the course of a experience, how a neuron translates its transcriptome charts its fate and function. The translation of specific mRNA can be dynamically regulated by signaling pathways, nutrient availability, misfolded protein accumulation, and neuronal activity.
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In the lab, we have deployed modern molecular techniques to understand how translation control mechanisms operate in neural cells and how their disruption causes neurological disorders.
S, Eacker
Ribosome profiling: a quantitative method to assess translation
To gain a genome-wide perspective on how neural cells regulate translation, we employ a method called ribosome profiling. Following a mild RNase digestion, we recover and sequence ribosome protected fragments (or footprints). Comparing with total mRNAseq from the same sample, we can derive the efficiency at which any given mRNA is translated.
S, Eacker
mTOR and human neural precursor specification
We have applied ribosome profiling to human embryonic stem cell derived neural precursor cells (hNPCs) to understand how the mechanistic target of rapamycin (mTOR) regulates the specification of subtypes of precursors. Dysregulation of mTOR signaling underlies numerous neurological disorders including epilepsy, intellectual disability, and autism. Our results so far point to an important role for mTOR-mediated translation control in the specification a particular subtype of hNPCs.
I.Wu
Cell-type specific Ribosome profiling
in vivo
Understanding how translation is regulated within the intact nervous system presents enormous challenges, not least of which is the diversity of cell types within any given structure in the brain.
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Combining the translating ribosome affinity purification method with ribosome profiling (described above) we have developed method that allows us to study translation in genetically defined cell types in the mouse brain. This method allows us to determine how translation is altered by behaviorally relevant stimuli in specific cell types. In combination with targeted mutations , we can dissect how translation control machinery regulates what proteins are synthesized in neurons.
Ribosome profiling gives us a nucleotide level resolution of translation. This resolution allows us to identify translated segments of the genome not previously characterized including non-canonical open reading frames upstream and downstream (uORFs and dORFs) of the canonical main open reading frame (mORF).
S, Eacker