Revisiting the neutral dynamics derived limiting guanine-cytosine content using human de novo point mutation data

IF 0.8 Q4 GENETICS & HEREDITY Meta Gene Pub Date : 2022-02-01 DOI:10.1016/j.mgene.2021.100994
Wentian Li , Yannis Almirantis , Astero Provata
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Abstract

We revisit the topic of human genome guanine-cytosine (G+C) content and adenine-thymine (A+T) content under neutral evolution. For this study, the “gold standard” de novo mutation data within the human genome is used to estimate the mutation rates, instead of using base substitution data between related species. We define the rates (coefficients) of de novo mutation events, which are estimated solely from the mutation event data. Based on the de novo mutations collected from the intergenic regions of control samples, we are able to calculate the limiting content of any genomic quantities, by calculating the components of the normalized eigenvector corresponding to the largest eigenvalue of the transpose of the mutational rates matrix. When a 3-by-3 mutational rate matrix is used, accounting for the G+C content, A+T content, and CpG density, their neutral limit at time infinity is obtained. We observe that the G+C content in the currently G+C rich regions drops less severely than in the G+C poor regions. This provides a potential mechanism to retain the current spatial variation of G+C content (isochore-like structure), and to resist against homogenization.

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重新审视中性动力学推导限制鸟嘌呤-胞嘧啶含量使用人类新生点突变数据
我们重新探讨了中性进化下的人类基因组鸟嘌呤-胞嘧啶(G+C)含量和腺嘌呤-胸腺嘧啶(A+T)含量。在本研究中,使用人类基因组内的“金标准”从头突变数据来估计突变率,而不是使用亲缘物种之间的碱基替换数据。我们定义了从头突变事件的比率(系数),它仅由突变事件数据估计。基于从对照样本的基因间区收集的新生突变,我们能够通过计算与突变率矩阵转置的最大特征值相对应的归一化特征向量的分量来计算任何基因组量的极限含量。当使用3 × 3突变率矩阵时,考虑G+C含量、a +T含量和CpG密度,得到它们在无限时的中性极限。我们观察到,当前G+C富区G+C含量的下降幅度小于G+C穷区。这提供了一种潜在的机制来保持当前G+C含量的空间变化(等序结构),并抵抗均质化。
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来源期刊
Meta Gene
Meta Gene Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
1.10
自引率
0.00%
发文量
20
期刊介绍: Meta Gene publishes meta-analysis, polymorphism and population study papers that are relevant to both human and non-human species. Examples include but are not limited to: (Relevant to human specimens): 1Meta-Analysis Papers - statistical reviews of the published literature of human genetic variation (typically linked to medical conditionals and/or congenital diseases) 2Genome Wide Association Studies (GWAS) - examination of large patient cohorts to identify common genetic factors that influence health and disease 3Human Genetics Papers - original studies describing new data on genetic variation in smaller patient populations 4Genetic Case Reports - short communications describing novel and in formative genetic mutations or chromosomal aberrations (e.g., probands) in very small demographic groups (e.g., family or unique ethnic group). (Relevant to non-human specimens): 1Small Genome Papers - Analysis of genetic variation in organelle genomes (e.g., mitochondrial DNA) 2Microbiota Papers - Analysis of microbiological variation through analysis of DNA sequencing in different biological environments 3Ecological Diversity Papers - Geographical distribution of genetic diversity of zoological or botanical species.
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