Short Tandem Repeats

My dissertation focused on the functional and adaptive role of microsatellites, and to investigate their role I used natural populations of common sunflower as a model system. Microsatellites, also called short tandem repeats (STRs), are highly mutable and abundant throughout eukaryotic genomes. While their role in human diseases is well-documented, their potential adaptive role is still debated. One way microsatellites may contribute to adaptation is through their influence on gene expression. We tested this hypothesis on nantural populations of the common sunflower (Helianthus annuus), a species that widespread across much of North America and well adapted to its local environments.

Through our work, we found substantial evidence that transcribed microsatellites (eSTRs) can impact gene expression levels. For example, our study using RNA-seq data from 95 individuals from different sunflower populations identified 479 eSTRs where allele length was significantly correlated with gene expression . Notably, these correlations often exhibited a stepwise pattern, supporting the “tuning knob model”, which proposes that gradual changes in microsatellite length can fine-tune gene expression and ultimately influence phenotypic traits. Our results also showed that most of the eSTRs were located in the UTRs, in locations ideal for regulating gene expression.

Our research has also explored the role of microsatellites in gene expression divergence among closely related Helianthus species. We compared transcriptomes of 50 individuals from five species and discovered a significant pattern: genes containing microsatellites in non-coding regions, such as UTRs, were more likely to be differentially expressed between species than genes with microsatellites in coding regions or those lacking microsatellites. This trend was consistent across all species pairs, suggesting non-coding microsatellites may be crucial in shaping gene expression divergence during speciation.

Further evidence points to the influence of microsatellites on gene regulation. We found that microsatellite-containing differentially expressed genes were significantly enriched for GO terms related to transcription regulation and transcription factor activity [3, 5]. This suggests microsatellites may play a key role in regulating genes involved in important biological processes that contribute to species differentiation [3].

We also observed greater genetic divergence in transcripts containing microsatellites compared to those without, as measured by pairwise F_ST at SNPs. This suggests that genes with microsatellites may be under different selective pressures, leading to increased genetic differentiation among species.

To further investigate the relationship between microsatellite length variation and gene expression, we conducted a targeted study focusing on five eSTRs in Helianthus annuus populations across a latitudinal gradient. We found a significant correlation between eSTR length and gene expression for an eSTR located within the CHUP1 gene, which is involved in chloroplast movement . This finding suggests that this specific eSTR might contribute to sunflower adaptation across different environments and that longer or shorter alleles may be favored in extreme environmental conditions,

Our research, combined with that of others, strongly suggests that microsatellites, particularly those located in transcribed regions, can contribute to both gene expression variation within populations and gene expression divergence between species. Our work highlights the potential importance of these often-overlooked genomic elements in adaptation and evolution.