Abstract 18253: Exploiting Natural Genetic Variation to Understand Transcriptional Programs of Inflammation
Introduction: Individuals have varied responses to the same stimulus in the context of pharmacology and disease. Enhancers are important regulators of transcription. However, the exact regulation of these responses remains largely unknown. To explore the underlying molecular mechanisms, we utilized 5 different mouse strains to mimic the variation between individuals and investigated how natural genetic variation affects transcription in the context of inflammation.
Hypothesis: Strain-specific loss of transcription factor binding to a specific enhancer at which there is no mutation in the binding site for that factor is due to a mutation in a nearby binding site for an essential collaborating factor.
Methods: For each strain, we harvested macrophages and treated them with KLA, an inflammatory stimulus. Then, we performed RNA and GRO-seq to analyze the transcriptome and nascent transcripts. Furthermore, we performed ChIP-seq for key transcription factors and histone marks, and ATAC-Seq to analyze global transcription factor binding and open chromatin. We analyzed mRNA expression levels between the different mouse strains and the impact of natural genetic variation on transcription factor binding motifs that directly influence the establishment of enhancers and therefore gene expression.
Results: Our RNA-seq analysis shows that 2922 genes (11%) are differentially expressed between the most divergent strains at baseline and 3022 genes (12%) upon KLA treatment. Also, our preliminary ChIP-seq analyses show 64632 baseline (49%) different enhancer binding events and 70426 KLA (51%) binding events between the most divergent strains. For example, ApoE expression is significantly downregulated in 3 of 5 strains where there is a loss of a key transcription factor binding in its enhancer region.
Conclusion: Natural genetic variation has a significant impact on enhancer selection and therefore gene expression. These observations support the concept that natural genetic variation can be exploited as a powerful ‘mutagenesis’ approach to investigate mechanisms of gene regulation. Furthermore, these studies are expected to provide insights into how non coding genetic variants contribute to risk of cardiovascular and other inflammatory diseases.
Author Disclosures: H.B. Chun: None. V. Link: None. C. Glass: None.
- © 2016 by American Heart Association, Inc.