Gene expression regulation in the adaptive evolution of the hypoxia-tolerant rodent Spalax
1 PhD project proposal in the IPP summer call 2019
Changes in regulatory elements of gene expression, in particular those found in cis-acting sequences (promotors, enhancers), are considered to have a prime role in the divergent evolution and differential adaptation of species. Little, however, is known about how cis-regulatory sequence divergence is responsible for complex phenotypic traits. The blind mole rat Spalax is a subterranean rodent, which has adapted to survive an extreme lack of oxygen. Interestingly, hypoxia tolerance is accompanied by a longevity and cancer resistance phenotype, and it is unclear how these phenotypes are connected on a molecular level. Extensive transcriptome data of hypoxic and normoxic Spalax tissues suggest that adaptation of the mole rat to harsh environmental conditions to a great extent occurred on the level of transcription regulation. Many candidate genes with plausible connections to the mole rat’s phenotype are expressed at elevated levels in Spalax tissue compared to rat. Hence, we intend to investigate the contribution of gene regulatory changes during Spalax evolution by linking existing gene expression data to changes in DNA sequence and epigenetic status of cis-regulatory regions.
PhD Project Proposal: Identification of cis-regulatory sequences and their molecular evolution in adaptation of the blind mole rat Spalax
The PhD project should initially address the following questions: Where are the functional gene regulatory elements (promoter, enhancers) in the Spalax genome, and which genes do they regulate? By which mode of evolutionary change did the cis-acting regulatory sequences of candidate genes evolve in hypoxia-tolerant versus –sensitive mammals? Later on, we want to study if observed, conspicuous changes in gene regulatory elements do indeed confer a selective adaptive advantage using in vitro cell culture systems. To start, we will define the landscape of gene regulatory regions in the sequenced Spalax genome by genomics techniques. Active enhancers and promoters will be identified in Spalax liver tissue using ATAC-Seq to measure chromatin accessibility, ChIP-Seq to determine histone modification hallmarks of active promoters and enhancers and Hi-C to identify promoter-enhancer interactions. These data will link regulatory sites to the genes and their RNA-Seq expression data. On the sequence level, we will bioinformatically study signatures of selective regimes in candidate cis-regulatory sequences by defining conserved regions (evolving under selective constraint) and regions evolving faster than neutral codon positions, possibly reflecting positive selection for adaptive change. In a long-term perspective, the possible adaptive effect of conspicuous sequence changes in cis-regulatory regions of candidate genes shall be tested experimentally in vitro in cell cultures, e.g. by applying reporter gene assays.
Publications relevant to the project:
Fang X, et al. (2014). Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun, 5: 3966.
Schmidt H, et al. (2016). Molecular evolution of antioxidant and hypoxia response in long-lived, cancer-resistant blind mole rats: The Nrf2-Keap1 pathway. Gene, 577: 293–298.
Schmidt H, et al. (2017). Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax – a liver transcriptomics approach. Sci Rep, 7: 14348.
Prof. Thomas Hankeln
Institute of Molecular Genetics
Johannes Gutenberg University Mainz