Wilson David G, Clatterbuck Soper Sarah F, Pineda Marbin A, Walker Robert L, Meltzer Paul S
bioRxiv. 2024 Nov 22:2024.11.22.624895. doi: 10.1101/2024.11.22.624895.
Acquisition of a telomere maintenance mechanism is essential for cancer cells. In a minority of tumors, telomeres are lengthened via Alternative Maintenance of Telomeres (ALT), a telomerase-independent pathway based on homologous recombination. ALT tumors have heavily rearranged genomes with many structural variants containing telomere repeats. To better understand the genetic evolution of these tumors, we seek to determine if certain genomic loci tend to spatially associate with telomeres in ALT and are especially liable to experience telomere recombination events as a result. Assays that reveal close spatial associations between genomic loci, such as SPRITE and Hi-C, have enabled extensive exploration of genomic spatial organization. However, as analysis pipelines for these next-generation sequencing-based assays typically discard reads aligning to repetitive elements, little is known about the spatial arrangement of telomeres and other repetitive loci in the nucleus. Here, we present TelSPRITE, a novel approach to extracting telomere contact frequencies from SPRITE data. We identify reads containing telomere repeats and sort them into a single bin, quantifying spatial contacts between the telomere bin and the rest of the genome. Our analysis reveals a strong dependency of telomere contact frequency on chromosomal distance from the telomere, consistent with the known effect of linear distance on 3-dimensional spatial contacts. Telomere contacts are also strongly enriched near centromeres, a phenomenon that may be reflective of spatial clustering of heterochromatic regions. ALT cell lines are globally enriched for telomere content and display distinctive intrachromosomal spikes in telomere contact frequency. Our customized analysis of long read sequencing data suggests that loci with high telomere contact frequencies represent structural variants containing telomere repeats in ALT cells. Collectively, our results demonstrate general principles of telomeric spatial organization while also profiling the spectrum of genomic rearrangements in ALT cells.
获得端粒维持机制对癌细胞至关重要。在少数肿瘤中，端粒通过端粒替代维持（ALT）途径延长，这是一种基于同源重组的不依赖端粒酶的途径。ALT肿瘤具有高度重排的基因组，有许多包含端粒重复序列的结构变异。为了更好地理解这些肿瘤的遗传进化，我们试图确定某些基因组位点是否倾向于在ALT中与端粒在空间上相关联，并因此特别容易发生端粒重组事件。揭示基因组位点之间紧密空间关联的分析方法，如SPRITE和Hi-C，已经能够广泛探索基因组空间组织。然而，由于基于这些下一代测序分析的分析流程通常会丢弃与重复元件比对的读数，人们对端粒和细胞核中其他重复位点的空间排列知之甚少。在这里，我们提出了TelSPRITE，一种从SPRITE数据中提取端粒接触频率的新方法。我们识别包含端粒重复序列的读数，并将它们分类到一个单独的 bins 中，量化端粒 bins 与基因组其余部分之间的空间接触。我们的分析揭示了端粒接触频率对与端粒的染色体距离有很强的依赖性，这与线性距离对三维空间接触的已知影响一致。端粒接触在着丝粒附近也高度富集，这一现象可能反映了异染色质区域的空间聚集。ALT细胞系在全球范围内端粒含量丰富，并在端粒接触频率上显示出独特的染色体内峰值。我们对长读测序数据的定制分析表明，端粒接触频率高的位点代表ALT细胞中包含端粒重复序列的结构变异。总的来说，我们的结果证明了端粒空间组织的一般原则，同时也描绘了ALT细胞中基因组重排的谱图。
