调查古基因组中与食品生产相关的 DNA 甲基化变化:技术噪音之外缺乏一致的信号。

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Sevim Seda Çokoğlu, Dilek Koptekin, Fatma Rabia Fidan, Mehmet Somel
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引用次数: 0

摘要

新石器时代的过渡给各大洲的人类带来了饮食和生活方式的重大改变。除了有据可查的生物考古学和遗传学影响之外,这些变化是否也对过去的人类群体产生了分子水平的表观遗传学影响一直是一个悬而未决的问题。事实上,可以通过死后损伤模式从经过 UDG 处理的古代 DNA 中推断出甲基化特征,但信噪比较低;因此,目前还不清楚已发表的古基因组是否能提供必要的分辨率,以发现生活方式和饮食习惯转变的系统性影响。为了解决这个问题,我们汇编了来自欧亚大陆西部和北部的 13 个新石器时代前狩猎采集者(HGs)和 21 个新石器时代农民(NFs)的 UDG 处理过的猎枪基因组,这些基因组由 6 个不同的实验室发表,覆盖率约为 1×-58×(中位数 = 9×)。我们使用 epiPALEOMIX 和蒙特卡洛归一化方案来估算每个基因组的甲基化水平。我们的古甲基组数据集显示了预期的全基因组甲基化模式,如 CpG 岛低甲基化。然而,使用各种方法对数据进行分析后,并没有发现任何有关生存类型、遗传性别或组织效应的系统信号。将我们数据集中的 HG-NF 甲基化差异与现代中非狩猎采集者与农民之间的甲基化差异进行比较,也没有得出一致的结果。与此同时,古基因组图谱确实因其原产地实验室的不同而产生了强烈的聚类。要从古基因组中捕捉到与环境相关的微妙生物信号,可能需要使用更大的数据量、最大限度地减少技术噪音和/或使用替代方案。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×–58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.

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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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