Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing.
Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing.
复制标题
通过双重测序研究拟南芥中的低频体细胞突变。
DOI：
10.1101/2024.01.31.578196
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Sloan,DanielB
中科院分区：
文献类型：
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作者：
Waneka,Gus;Pate,Braden;Monroe,JGrey;Sloan,DanielB
突变是新的遗传多样性的来源，但也可能导致疾病和适应不良。传统观点认为，突变是随机发生的，相对于它们的环境特异性适应性后果。然而，由于转录偶联修复和基于局部表观基因组修饰，基因组内突变率可以显著变化，其在基因组中不均匀分布。与减少的突变相关的一个序列特征是更高的表达水平，其可以根据环境线索而变化。为了了解表达水平和突变率之间的关联是否与环境特异性适应性效应产生系统关系，我们通过热处理在拟南芥中扰动表达。我们定量基因表达以鉴定差异表达的基因，然后使用双链测序进行突变检测。这种方法提供了一个高度准确的测量频率的罕见体细胞突变的营养植物组织，这一直是最近的来源不确定性在植物突变研究。我们纳入了缺乏错配修复（MMR）和碱基切除修复（BER）能力的突变株系，以了解修复机制如何驱动偏倚突变积累。我们发现野生型（WT）和BER突变频率非常低（平均变异频率分别为1.8×10−8和2.6×10−8），而MMR突变频率显著升高（1.13×10−6）。这些结果表明，WT植物中体细胞变异频率极低，这表明需要更大的数据集来解决基本的进化问题，即环境变化是否会导致基因特异性突变率的变化。
Mutations are the source of novel genetic diversity but can also lead to disease and maladaptation. The conventional view is that mutations occur randomly with respect to their environment-specific fitness consequences. However, intragenomic mutation rates can vary dramatically due to transcription coupled repair and based on local epigenomic modifications, which are non-uniformly distributed across genomes. One sequence feature associated with decreased mutation is higher expression level, which can vary depending on environmental cues. To understand whether the association between expression level and mutation rate creates a systematic relationship with environment-specific fitness effects, we perturbed expression through a heat treatment in Arabidopsis thaliana. We quantified gene expression to identify differentially expressed genes, which we then targeted for mutation detection using Duplex Sequencing. This approach provided a highly accurate measurement of the frequency of rare somatic mutations in vegetative plant tissues, which has been a recent source of uncertainty in plant mutation research. We included mutant lines lacking mismatch repair (MMR) and base excision repair (BER) capabilities to understand how repair mechanisms may drive biased mutation accumulation. We found wild type (WT) and BER mutant mutation frequencies to be very low (mean variant frequency 1.8×10−8 and 2.6×10−8, respectively), while MMR mutant frequencies were significantly elevated (1.13×10−6). These results show that somatic variant frequencies are extremely low in WT plants, indicating that larger datasets will be needed to address the fundamental evolutionary question as to whether environmental change leads to gene-specific changes in mutation rate.