DNA methylation profiling in mummified human remains from the eighteenth-century.
Ontology highlight
ABSTRACT:
SUBMITTER: Schmidt M
PROVIDER: S-EPMC8322318 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimen from mummies of the 18th century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we detected characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions were in line with the fact that the specimen was lung tissue of a female 28-year-old donor. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.
2021-08-04 | GSE169595 | GEO
Project description:DNA Methylation Profiling in Mummified Human Remains from the Eighteenth-Century
| PRJNA717168 | ENA
Project description:In the absence of genetic diversity, plants rely on the capacity of phenotypic plasticity to cope with shifts in environmental conditions. Understanding the mechanisms behind phenotypic plasticity and how local phenotypic adjustments are transferred to clonal offspring, will provide insight into its ecological and evolutionary significance. Epigenetic changes have recently been proposed to play a crucial role in rapid environmental adaptation. While the contribution of epigenetic changes to phenotypic plasticity has been extensively studied in sexual reproducing model organisms, little work has been done on vegetative generations of asexual reproducing plant species. We studied the variability of DNA methylation and bud set phenology of the Lombardy poplar (Populus nigra cv. Italica Duroi), a cultivated tree representing a single genotype worldwide distributed since the eighteenth century. Bud set observations and CpG methyl polymorphisms were studied on vegetative offspring resulting from cuttings grown for one season in a common glasshouse environment. The cuttings were collected from 60 adult Lombardy poplars growing in different environments. The physiological condition of the cuttings was determined by measuring weight and nutrient condition. Methylation sensitive amplified polymorphisms were used to obtain global patterns of DNA methylation. Using logistic regression models, we investigated correlations among epigenotype, bud phenology, and the climate at the home site of the donor trees, while accounting for physiological effects. We found significant epigenetic variation as well as significant variation in bud phenology, in the absence of genetic variation. Remarkably, phenology of bud set observed at the end of the growing season in the common environment was significantly correlated with climate variables at the home site of the mother trees, specifically the average temperature of January and monthly potential evapotranspiration. Although we could not directly detect significant effects of epigenetic variation on phenology, our results suggest that, in the Lombardy poplar, epigenetic marks contribute to the variation of phenotypic response that can be transferred onto asexually reproduced offspring resulting in locally adapted ecotypes. This contributes to the growing evidence that epigenetic-based transgenerational inheritance might be relevant for adaptation and evolution in contrasting or rapidly changing environments.
| S-EPMC6242946 | biostudies-literature
Project description:Adult stature has become a widely used indicator of childhood nutritional status in historical populations and may provide insights into health inequalities that are not discernible in mortality rates. However, most pre-twentieth-century British data on heights suffer from selection biases. Here we present unique evidence on heights of adult males by occupation from an unbiased sample of adult males in Dorset in 1798-99. The mean height of fully grown (married) men was very similar to that of older military recruits, and our sample therefore confirms the taller stature of English males relative to males of other European countries in the same period. In contrast to previous evidence of negligible or U-shaped socio-economic gradients in mortality in this period, we found a fairly linear gradient in height by socio-economic status, that is similar in magnitude to class differences in adult height among English males born in the mid-twentieth century.Supplementary material for this article is available at: https://doi.org/10.1080/00324728.2020.1823011.
| S-EPMC8516076 | biostudies-literature
Project description:Background and aimsMutations in TERT (telomerase reverse transcriptase) promoter are established gatekeepers in early hepatocarcinogenesis, but little is known about other molecular alterations driving this process. Epigenetic deregulation is a critical event in early malignancies. Thus, we aimed to (1) analyze DNA methylation changes during the transition from preneoplastic lesions to early HCC (eHCC) and identify candidate epigenetic gatekeepers, and to (2) assess the prognostic potential of methylation changes in cirrhotic tissue.Approach and resultsMethylome profiling was performed using Illumina HumanMethylation450 (485,000 cytosine-phosphateguanine, 96% of known cytosine-phosphateguanine islands), with data available for a total of 390 samples: 16 healthy liver, 139 cirrhotic tissue, 8 dysplastic nodules, and 227 HCC samples, including 40 eHCC below 2cm. A phylo-epigenetic tree derived from the Euclidean distances between differentially DNA-methylated sites (n = 421,997) revealed a gradient of methylation changes spanning healthy liver, cirrhotic tissue, dysplastic nodules, and HCC with closest proximity of dysplasia to HCC. Focusing on promoter regions, we identified epigenetic gatekeeper candidates with an increasing proportion of hypermethylated samples (beta value > 0.5) from cirrhotic tissue (<1%), to dysplastic nodules (≥25%), to eHCC (≥50%), and confirmed inverse correlation between DNA methylation and gene expression for TSPYL5 (testis-specific Y-encoded-like protein 5), KCNA3 (potassium voltage-gated channel, shaker-related subfamily, member 3), LDHB (lactate dehydrogenase B), and SPINT2 (serine peptidase inhibitor, Kunitz type 2) (all P < 0.001). Unsupervised clustering of genome-wide methylation profiles of cirrhotic tissue identified two clusters, M1 and M2, with 42% and 58% of patients, respectively, which correlates with survival (P < 0.05), independent of etiology.ConclusionsGenome-wide DNA-methylation profiles accurately discriminate the different histological stages of human hepatocarcinogenesis. We report on epigenetic gatekeepers in the transition between dysplastic nodules and eHCC. DNA-methylation changes in cirrhotic tissue correlate with clinical outcomes.
| S-EPMC8144238 | biostudies-literature
Project description:Migration is a central component of both individual life-courses and macro-level demographic systems. In the absence of population registers and other surveillance systems, however, it is often difficult to measure. This is especially the case in historical populations. Compared to measures of fertility, nuptiality and mortality, then, migration processes are rather less studied. Recent studies in the English historical context have challenged long standing theoretical constructs concerning the relationship between migration and modernisation; gender and distance travelled; motivation for movement and the very nature of the movers themselves. Using a set of marriage registers for a large, agricultural county, this study explores intra-county migration among a predominantly young population over the period 1700 to 1836. The proportion of migrants is explored as well as the distance between 'home' and 'marriage' parishes. For perhaps the first time, chord diagrams are deployed for historical English migration data to visualise inter- and intra- regional/district migration. Although there are numerous limitations concerning the scope of the sample and the study, the evidence presented here broadly accords with recent studies of migration in pre-industrial England; and shows the potential to both use circular visualisation and exploit large scale samples of marriage registers to gain a further insight into a particular type of historical migration.
| S-EPMC7689171 | biostudies-literature
Project description:Mummified human tissues are of great interest in forensics and biomolecular archaeology. The aim of this study was to analyse post mortem DNA alterations in soft tissues in order to improve our knowledge of the patterns of DNA degradation that occur during salt mummification. In this study, the lower limb of a female human donor was amputated within 24 h post mortem and mummified using a process designed to simulate the salt dehydration phase of natural or artificial mummification. Skin and skeletal muscle were sampled at multiple time points over a period of 322 days and subjected to genetic analysis. Patterns of genomic fragmentation, miscoding lesions, and overall DNA degradation in both nuclear and mitochondrial DNA was assessed by different methods: gel electrophoresis, multiplex comparative autosomal STR length amplification, cloning and sequence analysis, and PCR amplification of different fragment sizes using a damage sensitive recombinant polymerase. The study outcome reveals a very good level of DNA preservation in salt mummified tissues over the course of the experiment, with an overall slower rate of DNA fragmentation in skin compared to muscle.
| S-EPMC4206501 | biostudies-literature
Project description:Researchers have debated the relative importance of environmental versus Indigenous effects on past fire regimes in eastern North America. Tree-ring fire-scar records (FSRs) provide local-resolution physical evidence of past fire, but few studies have spatially correlated fire frequency from FSRs with environmental and anthropogenic variables. No study has compared FSR locations to Native American settlement features in the eastern United States. We assess whether FSRs in the eastern US are located near regions of past Native American settlement. We also assess relationships between distance to Native American settlement, environmental conditions, and fire frequency in central Pennsylvania (PA), US, using an "ensemble of small models" approach for low sample sizes. Regression models of fire frequency at 21 locations in central PA often selected distance-based proxies of Indigenous land use. Models with mean annual temperature and Native American variables as predictors explained > 70% of the variation in fire frequency. Alongside temperature and wind speed, "distance to nearest trail" and "mean distance to nearest town" were significant and important predictors. In 18th-century central PA, fires were more frequent near Indigenous trails and towns, and further south due to increasing temperature and pyrophilic vegetation. However, for the entire eastern US, FSRs are located far from past settlement, limiting their effectiveness in detecting fire patterns near population centers. Improving understanding of historical fire will require developing FSRs closer to past Native American settlement.
| S-EPMC10616284 | biostudies-literature
Project description:The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
| S-EPMC4798955 | biostudies-literature
Project description:DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of six annotation categories showed that evolutionarily conserved regions are the predominant sites for differential DNA methylation and that a core region surrounding the transcriptional start site is an informative surrogate for promoter methylation. We find that 17% of the 873 analyzed genes are differentially methylated in their 5' UTRs and that about one-third of the differentially methylated 5' UTRs are inversely correlated with transcription. Despite the fact that our study controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought.
| S-EPMC3082778 | biostudies-literature