Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.
Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea.
Nucleic Acids Res. 2024 Nov 11;52(20):12456-12474. doi: 10.1093/nar/gkae842.
Telomeres protect chromosome ends from DNA damage responses, and their dysfunction triggers genomic alterations like chromosome fusion and rearrangement, which can lead to cellular death. Certain cells, including specific cancer cells, adopt alternative lengthening of telomere (ALT) to counteract dysfunctional telomeres and proliferate indefinitely. While telomere instability and ALT activity are likely major sources of genomic alteration, the patterns and consequences of such changes at the nucleotide level in ALT cells remain unexplored. Here we generated haplotype-resolved genome assemblies for type I ALT mouse embryonic stem cells, facilitated by highly accurate or ultra-long reads and Hi-C reads. High-quality genome revealed ALT-specific complex chromosome end structures and various genomic alterations including over 1000 structural variants (SVs). The unique sequence (mTALT) used as a template for type I ALT telomeres showed traces of being recruited into the genome, with mTALT being replicated with remarkably high accuracy. Subtelomeric regions exhibited distinct characteristics: resistance to the accumulation of SVs and small variants. We genotyped SVs at allele resolution, identifying genes (Rgs6, Dpf3 and Tacc2) crucial for maintaining ALT telomere stability. Our genome assembly-based approach elucidated the unique characteristics of ALT genome, offering insights into the genome evolution of cells surviving telomere-derived crisis.
端粒保护染色体末端免受 DNA 损伤反应的影响，其功能障碍会引发染色体融合和重排等基因组改变，从而导致细胞死亡。某些细胞，包括特定的癌细胞，会采用端粒的替代延长（ALT）来对抗功能失调的端粒并无限期增殖。虽然端粒不稳定和 ALT 活性可能是基因组改变的主要来源，但在 ALT 细胞中，核苷酸水平上的这些变化的模式和后果仍未被探索。在这里，我们通过高度准确或超长读取和 Hi-C 读取，为 I 型 ALT 小鼠胚胎干细胞生成了单倍型解析基因组组装。高质量的基因组揭示了 ALT 特异性的复杂染色体末端结构和各种基因组改变，包括 1000 多个结构变体（SVs）。作为 I 型 ALT 端粒模板使用的独特序列（mTALT）显示出被招募到基因组中的痕迹，mTALT 的复制具有惊人的准确性。亚端粒区域表现出明显的特征：抵抗 SV 和小变体的积累。我们以等位基因分辨率对 SV 进行了基因分型，鉴定出了对维持 ALT 端粒稳定性至关重要的基因（Rgs6、Dpf3 和 Tacc2）。我们基于基因组组装的方法阐明了 ALT 基因组的独特特征，为研究在端粒衍生危机中幸存下来的细胞的基因组进化提供了思路。
