Abstract
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from ‘Evolution Canyon’ in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels. We also demonstrate that while temperature affects editing levels at more sites than genetic differences, genetically regulated sites tend to be less affected by temperature. This work shows the extent to which gene expression and RNA editing differ between flies from different microclimates, and provides insights into the regulation responsible for these differences.
Highlights
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution
We performed principal component analysis (PCA) using data from ~2 million SNPs identified from whole-genome sequencing (WGS) (Fig. 1b)
Since the lines in the NFS1 group are separated from the rest of the flies on the PC1 axis, which explains the most variation in the data set (15.3%), and since the NFS1 group contains more flies than the NFS2 group, we considered the flies in the NFS1 group to most accurately represent the north-facing slope (NFS) flies
Summary
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. Inosine gets recognized as guanosine during translation, so A-to-I RNA editing has the potential to alter amino acid sequences of proteins and affect other transcriptional processes[6,7,8] It is especially important for proper neuronal function; for instance, mice lacking ADAR2 die of seizures early in life[9], and flies lacking ADAR display a host of neurological phenotypes, including age-dependent neurodegeneration, problems with locomotion, as well as courtship and circadian rhythm defects[10,11]. Previous work in our lab and others shows the importance of genetic cis-regulation in comparing editing levels between different Drosophila species[13], and in Drosophila that come from a common environment[14,15], while other work in flies has shown that RNA editing changes in response to temperature[16,17]. We form a more complete picture about the various contributions to gene expression and RNA editing differences in flies from Evolution Canyon, results that can potentially be applied to other species and climates
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