National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Mol Biol Evol. 2023 Aug 3;40(8). doi: 10.1093/molbev/msad176.
Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of CEN in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat CEN. We found that most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core CEN. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned CEN. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize CEN. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.
着丝粒（CEN）是在维持基因组稳定性中起关键作用的染色体区域。大多数真核生物中高度重复的 DNA 序列可以快速进化，并促进核型进化。尽管这些序列具有可变性，但人们并不完全了解这些广泛变化的序列如何确保着丝粒功能的内稳态。在这项研究中，我们调查了来自全球育种计划的小麦品系群体中的 CEN 的遗传学和表观遗传学。我们捕获了大而复杂的小麦 CEN 中高度重复的序列、定位和表观遗传变异。我们发现，大多数 CENH3 相关重复序列是反转录转座子的 Cereba 元件，并且在不同的小麦品系中表现出系统发育上的同质化，但相关性较低的重复序列在各自的小麦品系中以自己的方式分化，这意味着存在特定的机制来选择某些重复类型作为功能核心 CEN。此外，我们观察到 CENH3 核小体结构在复杂着丝粒重复序列（包括重定位的 CEN）上显示出 DNA 末端更宽松的缠绕。我们还发现严格的 CENH3 核小体定位和内在的 DNA 特征在不同品系中决定着丝粒身份方面起着作用。特定的非 B 型 DNA 与重定位的着丝粒的 CENH3 核小体有很大的关联。这些发现表明，在不同的基因组背景下，CENH3 核小体的适应涉及多种机制，这些机制可以稳定 CEN。最终，我们提出了在多样化的基因组背景下着丝粒染色质具有显著的表观遗传可塑性，并且由于过去的育种选择，高度的稳健性对于维持小麦 10+品系中的着丝粒功能和基因组稳定性至关重要。
