Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus)

Divergence of gene expression is known to contribute to the differentiation and separation of populations and species, although the dynamics of this process in early stages of population divergence remains unclear. We analyzed gene expression differences in three organs (brain, liver, and testis) between two natural populations of Mus musculus domesticus that have been separated for at most 3000 years. We used two different microarray platforms to corroborate the results at a large scale and identified hundreds of genes with significant expression differences between the populations. We find that although the three tissues have similar number of differentially expressed genes, brain and liver have more tissue–specific genes than testis. Most genes show changes in a single tissue only, even when expressed in all tissues, supporting the notion that tissue–specific enhancers act as separable targets of evolution. In terms of functional categories, in brain and to a smaller extent in liver, we find transcription factors and their targets to be particularly variable between populations, similar to previous findings in primates. Testis, however, has a different set of differently expressed genes, both with respect to functional categories and overall correlation with the other tissues, the latter indicating that gene expression divergence of potential importance might be present in other datasets where no differences in fraction of differentially expressed genes were reported. Our results show that a significant amount of gene expression divergence quickly accumulates between allopatric population

Tekil hücre genom analizi yoluyla sağlıklı ve hasta bireylerin beyinlerinin incelenmesi

TÜBİTAK KBAG Proje01.12.2018Alzheimer Hastalığı (AH) genetik, çevresel ve rastgele etmenlere bağlı olarak gelişenkarmaşık ve ölümcül bir hastalıktır. AH'nin sebepleri ve gelişim süreci halen çok sınırlı ölçüdeanlaşılmıştır.Geçtiğimiz onyıllarda geleneksel sitometri ve FISH gibi yöntemler kullanan çalışmalar, AHvakaları ve sağlıklı kontrol bireyleri karşılaştırmış, AH vakalarının nöronlarında anlamlı ölçüdeyüksek seviyede anöploidi ve megabaz büyüklüğünde kopya sayısı varyasyonu (KSV)bulmuştur. Ancak bu yöntemlerin teknik gürültüye açık olması sonuçların güvenirliğinisınırlamıştır.Bu çalışmanın amacı da AH vakalarında somatik KSV yükünün rolü olabileceği hipotezini,tekil hücre tüm genom dizilemesi yöntemi kullanarak test etmektir. Ayrıca bilgimiz dahilinde ilkdefa bu çalışmada genom dizileme işlemi için nöron çekirdeklerini toplarken, özgün hücrelerinseçilmesine izin veren lazerle kesme ve yakalama (LCM) yöntemi kullanılmıştır.Çalışmamız kapsamında 10 AH vakası ile aynı yaş aralığında ve sağlıklı 7 kontrol bireyintemporal korteks ve hipokampüs örneklerinden elde edilen nöronal çekirdeklerden, iki farklıyöntemle toplam 1190 kütüphane oluşturulmuş ve düşük seviyede Illumina platformundadizilenmiştir. Bunlar arasından 472 hücreye ait veriler kalite ve gürültü filtrelerini geçebilmiştir.Analizimizin sonuçları, literatürde son yıllarda yayımlanan benzer verilerle de beraberdeğerlendirilerek, birkaç başlıkta özetlenebilir: Birincisi, megabaz uzunluğunda somatikKSV'ler insan beyin nöronları arasında %10 veya daha düşük orandadır. Tüm kromozomanöploidiler ise %2 veya daha düşük oranda görülmektedir. İkincisi, yakın zamanlı benzer birçalışmayla paralel olarak, AH ve kontrol bireyleri arasında anlamlı bir fark bulunmamaktadır.Teknik açıdan ise, çekirdekleri ayrıştırma işleminde LCM, FACS'a göre anlamlı ölçüde dahagürültülü bir yöntemdir. Ayrıca teknik gürültü tekil genom analizinde de (muhtelemen dizilemederinliğinden bağımsız olarak) ciddi bir sorundur.Tekil nöronların genom varyasyonunun ve somatik çeşitliliğin AH'de rolünün incelenmesinihedefleyen gelecek çalışmalar, gürültüyü minimize eden yöntemlerle makro değil mikromutasyonları incelemeyi hedefleyebilir.Alzheimer's Disease (AD) is a complex and deadly pathology that develops through theinfluence of genetic, environmental and stochastic factors. Its etiology is still only partlyunderstood. Within the last decades, a number of studies using classical methods such ascytometry or FISH have compared AD patients and healthy controls, to find that AD patients'neurons carry a significantly higher proportion of aneuploidy and megabase-scale copynumber variation (CNV). However the vulnerability of these methods to technical noise haslimited their credibility.The aim of this study has been to test the hypothesis that somatic CNV load may have a rolein AD using single cell whole genome sequencing. In addition, to our knowledge for the firsttime in this study, the laser-capture microdissection (LCM) method has been used forisolating nuclei of specific neurons for genome sequencing.We have generated a total of 1190 libraries from neuronal nuclei, derived from temporalcortex and hippocampus samples of 10 AD patients and 7 healthy age-matched controlindividuals, and performed low coverage Illumina sequencing. In total 472 cells data havepassed our data quality and noise filters.In conjunction with recent reports, our results can be summarised as follows: First,megabase-scale CNV's are most likely at 10% or lower frequency among human neurons.Whole chromosome aneuploidies are 2% or lower. Second, in line with a recent similarstudy, we cannot find any indication of higher CNV among AD patients' neurons than healthycontrol neurons. On the technical side, LCM appears to be a significantly more noisy methodthan FACS for isolation of nuclei. Further, technical noise haunts single cell genomeanalyses, most likely independent of sequencing depth.Future studies aiming to investigate the possible roles of single cell genomic variation andsomatic diversity in AD may prefer to use methods that particularly minimise noise and tofocus on micro, instead of macro mutations

Temporal changes in the gene expression heterogeneity during brain development and aging

Cells in largely non-mitotic tissues such as the brain are prone to stochastic (epi-)genetic alterations that may cause increased variability between cells and individuals over time. Although increased interindividual heterogeneity in gene expression was previously reported, whether this process starts during development or if it is restricted to the aging period has not yet been studied. The regulatory dynamics and functional significance of putative aging-related heterogeneity are also unknown. Here we address these by a meta-analysis of 19 transcriptome datasets from three independent studies, covering diverse human brain regions. We observed a significant increase in inter-individual heterogeneity during aging (20 + years) compared to postnatal development (0 to 20 years). Increased heterogeneity during aging was consistent among different brain regions at the gene level and associated with lifespan regulation and neuronal functions. Overall, our results show that increased expression heterogeneity is a characteristic of aging human brain, and may influence aging-related changes in brain functions

Effects of coumaphos on locomotor activities of different honeybee (Apis mellifera L.) subspecies and ecotypes

The effects of acute sublethal doses of coumaphos, an acaricide used against Varroa destructor infestation in beekeeping, on the locomotor activities of four native honeybee subspecies of Türkiye including two ecotypes (Carniolan honeybee -A. m. carnica, Syrian honeybee -A. m. syriaca, Caucasian honeybee- A. m. caucasica, and Muğla and Yığılca ecotypes of Anatolian honeybee A. m. anatoliaca) were investigated using an individual locomotor activity monitoring system. Analysis of locomotor activity data in the first 12-h, last 12-h, and 24-h time periods showed that bees from caucasica and carnica subspecies were not affected by coumaphos at all three acute doses (1, 2, and 5 μg coumaphos in 10 μl sucrose syrup for each bee). In contrast, bees from A. m. syriaca subspecies showed significantly elevated locomotor activity levels at 2 and 5 μg coumaphos doses within the first 12 h. Bees from both Muğla and Yığılca ecotypes of anatoliaca subspecies also showed elevated locomotor activity levels at 5 μg coumaphos dose but the magnitude of increase was lower in these ecotypes compared to that seen in syriaca subspecies in the first 12-h period. In general, increasing doses of coumaphos resulted in increased locomotor activity (locomotor activity), with differences in sensitivity across honeybee populations. Possible mechanisms underlying this variance and suggestions for further studies are discussed

Variation and Functional Impact of Neanderthal Ancestry in Western Asia

Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out of Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine present-day Europeans. Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey. Our results confirmed previous observations that contemporary Western Asian populations, on an average, have lower levels of Neanderthal-introgressed DNA relative to other Eurasian populations. Modern Western Asians also show comparatively high variability in Neanderthal ancestry, which may be attributed to the complex demographic history of the region. We further replicated the previously described depletion of putatively functional sequences among Neanderthal-introgressed haplotypes. Still, we find dozens of common Neanderthalintrogressed haplotypes in the Turkish sample associated with human phenotypes, including anthropometric and metabolic traits, as well as the immune response. One of these haplotypes is unusually long and harbors variants that affect the expression of members of the CCR gene family and are associated with celiac disease. Overall, our results paint a complex first picture of the genomic impact of Neanderthal introgression in the Western Asian populations

Molecular footprint of Medawar's mutation accumulation process in mammalian aging

Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging-related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age-related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up-regulated during aging. In general, the more often a gene is found up-regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up-regulated genes have overlapping functional properties that include responses to age-associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures

Whole Genome Sequencing of Turkish Genomes Reveals Functional Private Alleles and Impact of Genetic Interactions with Europe, Asia and Africa

Background Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×). Results We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. Conclusion This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey

Evolution of Neuronal and Endothelial Transcriptomes in Primates

The study of gene expression evolution in vertebrates has hitherto focused on the analysis of transcriptomes in tissues of different species. However, because a tissue is made up of different cell types, and cell types differ with respect to their transcriptomes, the analysis of tissues offers a composite picture of transcriptome evolution. The isolation of individual cells from tissue sections opens up the opportunity to study gene expression evolution at the cell type level. We have stained neurons and endothelial cells in human brains by antibodies against cell type-specific marker proteins, isolated the cells using laser capture microdissection, and identified genes preferentially expressed in the two cell types. We analyze these two classes of genes with respect to their expression in 62 different human tissues, with respect to their expression in 44 human “postmortem” brains from different developmental stages and with respect to between-species brain expression differences. We find that genes preferentially expressed in neurons differ less across tissues and developmental stages than genes preferentially expressed in endothelial cells. We also observe less expression differences within primate species for neuronal transcriptomes. In stark contrast, we see more gene expression differences between humans, chimpanzees, and rhesus macaques relative to within-species differences in genes expressed preferentially in neurons than in genes expressed in endothelial cells. This suggests that neuronal and endothelial transcriptomes evolve at different rates within brain tissue