MAX GRUBER

PI: Alon Goren, Ph.D., Department of Medicine, Division of Genetics

Systematic Analysis of the Impact of Short Tandem Repeats on Gene Expression

Short tandem repeats (STRs) are genomic sequences with a repeat unit of 1-6bp, representing an intriguing type of genetic variation given their polymorphisms and high mutation rate. Our lab has previously shown that variations in the repeat number of numerous STRs is associated with the expression of nearby genes. To experimentally study this observation, we employ a massively parallel reporter assay to test a series of promoter proximal human STRs. Our results reveal that CG-rich STRs exhibit induction of reporter activity that is higher than AT-rich ones, which is solely an effect of the repeat unit patterns, with no consensus trend in terms of STR length. Among the STRs that exhibited reporter activity, the majority demonstrated a positive correlation between repeat number and reporter expression. We additionally performed the experiment in multiple cell lines, and observe that some of the STRs are impacting gene expression in a celltype specific manner.

Analysis of Expression Patterns of Genes in Different Locations of the Brain

In every region of the brain, we are able to detect different levels of gene expression, and understanding how these differing results form from the same genetic code is vital towards understanding of neurodevelopment. We propose that it is possible to detect differing patterns of the gene expression when traveling through the brain’s regions in an anterior-posterior or dorsal-ventral direction. By generating neural maps of fifty-eight different genes found throughout these regions, we are able to generate spatial correspondence between gene expression. Current open-source programs, such as the spin test, assist us by generating permutations and helping us understand the relationship between cortical datasets. Another consideration is how regions are affected by sets of two factors: one tends to influence over frontal and temporal regions, and the other which tends to influence over occipital and parietal regions, along with regions such as the precuneus which is influenced by both.

PI: Christina J.

Sigurdson, DVM,

PhD, Departments of Pathology and Medicine, UC San Diego

Mechanisms of Prion Protein-Induced Neurodegeneration in the Central Nervous System of Drosophila melanogaster

Prion diseases are fatal neurodegenerative disorders characterized by neuronal loss and the accumulation of prion protein aggregates (PrPSc) in the brain. PrPc, the normal cellular prion protein, has been implicated in binding oligomers, including PrPSc that form in patient brains, leading to neurotoxicity. The mechanism by which PrPc interacts with PrPSc to cause neuronal loss is unclear. The 92N-PrPc point mutation may help to elucidate the neurotoxic pathway, as it has been shown to result in spontaneous neuronal degeneration in mice. We generated transgenic 92N-PrP and wild type PrP-expressing Drosophila. Western blot revealed that the 92N-PrPc is expressed in flies. Lifetime and climbing assays were used to test behavioral differences. These experiments show the generation of a mutant prion protein expressing Drosophila, and future experiments will focus on assessing the behavior changes, histopathologic lesions, and toxic signaling pathways towards a goal of understanding how mutant prion protein induces neuronal death.