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Clock gene polymorphisms in Drosophila; natural selection and function


About This PhD Project

Project Description

The molecular function of circadian clock genes are well understood and conserved from flies to mammals, but the implications of natural variation in clock gene sequences are only recently becoming evident. Human clock gene polymorphisms lead to delayed/advanced sleep phase syndromes, and some variants have been implicated in depression and metabolic disorders. Evolutionary studies have revealed the DNA signature of natural selection in Europeans but not Africans in period, which is the light-sensing canonical clock component. This suggests that period sequences adapted to the novel photoperiodic environment of high-latitude Europe after the human migrations from the non-photoperiodic sub-Saharan African savannah ~60-100,000 years ago. In Drosophila, which also migrated to Europe from sub-Saharan Africa ~12000 years ago, polymorphisms in the light-sensitive TIMELESS protein show evidence for directional selection due to differential changes in the photoperiodic sensitivity of the clock, mirroring the result with humans (Tauber et al 2007 Science, Sandrelli et al Science).

In Drosophila period, a repeat-length coding polymorphism is maintained by balancing selection because of differential responses of the clock to environmental temperatures, which is in turn mediated by the different degradation dynamics of the polymorphic PER proteins (Sawyer et at 1997, Science). The corresponding PER region in humans is also polymorphic in length and has implications for morning or eveningness, characteristics that are modulated by the stability of mammalian PER. As usual, Drosophila studies predate work in mammals and direct attention towards the roles of these polymorphisms in adapting the organism to its environment, illuminating the functions of the polymorphic domains of the clock proteins and leading to an understanding of the evolutionary history of the clock.

More recently, NGS approaches have identified additional variation among several more members of the Drosophila clock machinery in both the Old and the New Worlds. In addition, the 1000 genomes project has identified large numbers of polymorphisms in human clock genes. This sequence information in both species has yet to be systematically mined. Our project has the following components:
1. Bioinformatic analysis of Drosophila and human clock genes. We will annotate the coding sequence variation in the two species’ clock genes. Haplotypes are available for both species and it will be possible to generate frequency spectra of the common variants and also examine whether they are geographically structured. We would find the interesting variants in both species, compare them and investigate whether there might be gene regions of interest that correspond between them.

2. Signatures of selection. Drosophila is an experimentally tractable model and any high frequency variants, particularly those that show spatial differentiation are ripe for further evolutionary and functional study. The use of neutrality tests on a genomic scale shall be used to identify Drosophila variants that might be under selection. Some of this work has already been done in that lists of fly genes that might show selective signatures exist, but nobody has systematically sorted through these data for clock genes.

3. Functional analysis of Drosophila clock genes. Once an interesting polymorphism has been identified (there is already preliminary data on Clock variants) we shall study rhythm phenotypes by comparing fly strains that differ in a particular polymorphic sequence in terms of free-running endogenous period, light responses of the clock, temperature responses, sleep, and other clock related phenotypes such as diapause (seasonal rhythms). CRISPR/Cas9 mediated mutagenesis, neurogenetics using gal4/UAS methods, and ICC will be used to identify the physiological/anatomical substrates that lead to polymorphic phenotypes.

Techniques that will be undertaken during the project

- Bioinformatics
- Population genetics
- Drosophila genetics
- Behavioural analyses
- Neurogenetic analysis of behaviour using Gal4/UAS
- Relevant cell-based biochemical/molecular assays (qPCR, westerns)
-confocal microscopy, ICC

Available to UK/EU applicants only
Application information
https://www2.le.ac.uk/research-degrees/doctoral-training-partnerships/bbsrc

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