Ancient Brazil
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB48809 | ENA |
REPOSITORIES: ENA
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Project description:Gene order, or microsynteny, is generally thought not to be conserved across metazoan phyla. Only a handful of exceptions, typically of tandemly duplicated genes such as Hox genes, have been discovered. Here, we performed a systematic survey for microsynteny conservation in 17 genomes and identified nearly 600 pairs of unrelated genes that have remained together across over 600 million years of evolution. Using multiple genome-wide resources, including several genomic features, epigenetic marks, sequence conservation and microarray expression data, we provide extensive evidence that many of these ancient microsyntenic arrangements have been conserved in order to preserve either (i) the coordinated transcription of neighboring genes, or (ii) Genomic Regulatory Blocks (GRBs), in which transcriptional enhancers controlling key developmental genes are contained within nearby “bystander” genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos to further investigate putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results show that ancient genomic associations are far more common in modern metazoans than previously thought – likely involving over 12% of the ancestral bilaterian genome – and that cis-regulatory constraints have played a major role in conserving the architecture of metazoan genomes. ChIP-seq H3K27me3 of 24hpf zebrafish embryos
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Project description:To investigate dairy consumption in ancient Mongolia, we analysed dental calculus samples from four Late Bronze Age (LBA, 1500-1000 BCE) individuals for proteomic evidence of milk proteins. As many archaeological sites before Mongolia's Iron Age suffer from a dearth of occupational materials, looking to biomolecular markers of dietary intake can open new investigational avenues into ancient economies. In this case, we use a previously established method of extracting proteins from calculus to explore the consumption of dairy products at LBA Khirigsuur sites in northern Mongolia's Hovsgol Aimag. Seven of nine individual's calculus contained peptides from the whey protein Beta-lactoglobulin from Ovis, Capra hircus, Bos, and general Bovidae species. Aside from proteomics, these and 16 other individuals from the site were analysed for aDNA. We found that 18 of the 20 were primarily from one genetic ancestral group, and Ancient North Eurasian (ANE). One of the outliers represents a combination of ANE and Western Steppe Herder (WSH), with the other a combination of ANE and Eastern Asian (EE). This finding, while important in its own right, evidences the earliest known dairy consumption in Mongolia, and supports a widely held assumption that pastoralism was a primary subsistence strategy in the ancient Eastern Steppes. The combined proteomic and DNA evidence suggest that Western Steppe dairy animals and technology entered Mongolia before genetic admixture.
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Project description:DE microRNAs between normal bone and ancient osteosarcoma
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