Biology subjects

Makinen, H.

Publications and source records attributed to Makinen, H..

5 recordsLinked to original sources

bioRxiv2022

DNA methylation regulates sex-biased gene expression in the house sparrow

Sexual dimorphism is often mediated by tissue-specific, differential gene expression, but the mechanisms that regulate these gene expression patterns are not well understood. Here, we investigate DNA methylation as a potential regulator of sex-biased gene expression in the house sparrow (Passer domesticus). First, we examine whether sex-bias in gene expression or DNA methylation is present in this species, and whether any sex differences are tissue-general or tissue-specific. Second, we assess the correlation between gene expression and DNA methylation at different genomic features in several tissues. Samples clustered by tissue type when looking at both gene expression and DNA methylation, and in gonads samples clustered according to sex. We demonstrate sex-bias in DNA methylation and gene expression on the Z-chromosome as well as on autosomes, but find that most of the sex-biased genes are tissue-specific and that the majority of sex-bias occurs in gonads, although some tissue-general sex differences were observed. This underscores the importance of choosing a tissue relevant to the studied phenotype in DNA methylation or gene expression studies. We find strong negative correlation between DNA methylation and gene expression at the transcription start site (TSS), and that the TSS of highly expressed genes is hypomethylated in comparison to the TSS of genes with low expression. Furthermore, we show that sex-biased DNA methylation can account for 14% of the sex differences in gene expression in gonads. Together these results indicate that DNA methylation differences between the sexes can provide a mechanistic explanation for sex-biased gene expression that likely contributes to trait sexual dimorphism in nature.

evolutionary biology↗

bioRxiv2019

The effect of experimental lead pollution on DNA methylation in a wild bird population

Anthropogenic pollution is known to negatively influence an organisms physiology, behavior and fitness. Epigenetic regulation, such as DNA methylation, has been hypothesized as one mechanism to mediate such effects, yet studies in wild species are lacking. We first investigated the effects of early-life exposure to the heavy metal lead (Pb) on DNA methylation levels in a wild population of great tits (Parus major), by experimentally exposing nestlings to lead at environmentally relevant levels. Secondly, we studied the effects of heavy metal exposure in a population close to a copper smelter, where birds suffer from pollution-related decrease in food quality. For both comparisons, the analysis of about million CpGs covering most of the annotated genes, revealed that regions enriched for developmental processes showed pollution-related changes in DNA methylation, but the results were not consistent with binomial and beta binomial regression. Our study indicates that post-natal anthropogenic heavy metal exposure can affect methylation levels of development related genes in a wild bird population.

molecular biology↗

bioRxiv2019

High-resolution synchrotron imaging studies of intact fresh roots reveal soil bacteria promoted bioremediation and bio-fortification

Plant-microbe interactions can be utilized in bio-based processes such as bioremediation and biofortification, either to remove hazardous radionuclides and heavy metals from the soil, or to increase the accumulation of desired elements into crops to improve their quality. Optimizing such elegant plant-microbe interactions requires detailed understanding of the chemical element compositions of fresh plant tissues at cellular organelle resolution. However, such analyses remain challenging because conventional methods lack the required spatial resolution, contrast or sensitivity. Using a novel combination of nanoscaleresolution 3D cryogenic synchrotron-light ptychography, holotomography and fluorescence tomography, we show how soil bacteria interact with Arabidopsis thaliana and promote the uptake of various metals. Co-cultivation with Pseudomonas sp. strain T5-6-I alters root anatomy and increases levels of selenium (Se), iron (Fe) and other micronutrients in roots. Our approach highlights the interaction of plants and microbes in bioremediation and biofortification on the subcellular level.

plant biology↗

bioRxiv2018

Genomic signatures of fine-scale local adaptation in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, behaviour, and immune defence-related genes.

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene-environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, behaviour, and immune defence. These included the large-effect age-at-matunty gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a genomic region strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to river flow volume and co-vanes with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.

evolutionary biology↗

bioRxiv2017

Modularity Facilitates Flexible Tuning Of Plastic And Evolutionary Gene Expression Responses During Early Divergence

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying co-expressed modules now enable systems genetics approaches also in non-model species for better understanding of gene expression responses during early divergence. Here, we combined gene co-expression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that co-expression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.

evolutionary biology↗