Characterizing SVs associated with striatum eQTLs and addiction phenotypes in diverse mouse genomes

Aditya Gupta

Document Type

Article

Publication Date

8-9-2024

Keywords

JMG

JAX Location

In: Student Reports, Summer 2024, The Jackson Laboratory

Abstract

Behavioral phenotypes, substance use disorders, and addiction are heritable traits which can be attributed with complex neurological presentations. Despite these associations, many genetic loci which directly contribute to addiction phenotypes remain unclear, and identification of causal genetic variants found within natural populations remains a difficult task. To identify molecular phenotypes responsible for addiction traits, comprehensive profiling of the associated brain regions is required. To investigate genomic regions responsible for changes in brain gene expression, we performed expression quantitative trait mapping of loci responsible for changes in striatum gene expression in the diversity outbred mouse panel. Regions responsible for differential striatum gene expression were profiled for structural variation (SV, genetic variants ≥ 50bp), a variant type historically underrepresented in next generation sequencing experiments and addiction studies. From these data, we investigated specific gene sets which contained striatum eQTLs associated with SVs of unique sequencing characteristics, including tandem repeat and transposable element variants. By coupling these data with publicly available single cell RNA sequencing data derived from the developing striatum, we identify cell type specific expression of gene sets correlated with unique SV type signatures, including those that facilitate dopaminergic responses.

Please contact the Joan Staats Library for information regarding this document.

COinS