Abstract：
With hundreds of copies of rDNA, it is unknown whether they possess sequence variations that form different types of ribosomes. Here, we developed an algorithm for long-read variant calling, termed RGA, which revealed that variations in human rDNA loci are predominantly insertion-deletion (indel) variants. We developed full-length rRNA sequencing (RIBO-RT) and in situ sequencing (SWITCH-seq), which showed that translating ribosomes possess variation in rRNA. Over 1,000 variants are lowly expressed. However, tens of variants are abundant and form distinct rRNA subtypes with different structures near indels as revealed by long-read rRNA structure probing coupled to dimethyl sulfate sequencing. rRNA subtypes show differential expression in endoderm/ectoderm-derived tissues, and in cancer, low-abundance rRNA variants can become highly expressed. Together, this study identifies the diversity of ribosomes at the level of rRNA variants, their chromosomal location, and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.
摘要：
有数百个rDNA拷贝，尚不清楚它们是否具有形成不同类型核糖体的序列变异。这里,我们开发了一种长读变体调用算法，称为RGA，这表明人类rDNA基因座的变异主要是插入缺失（indel）变体。我们开发了全长rRNA测序（RIBO-RT）和原位测序（SWITCH-seq），这表明翻译核糖体具有rRNA的变异。超过1,000个变体被低表达。然而,数十种变体丰富，并形成不同的rRNA亚型，在indel附近具有不同的结构，如通过长阅读rRNA结构探测与硫酸二甲酯测序相结合所揭示的。rRNA亚型在内胚层/外胚层来源的组织中显示差异表达，在癌症中，低丰度rRNA变体可以变得高度表达。一起,这项研究在rRNA变体水平上鉴定了核糖体的多样性，它们的染色体位置，和独特的结构以及核糖体变异与组织特异性生物学和癌症的联系。
