Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Cell Genom. 2024 Sep 11;4(9):100629. doi: 10.1016/j.xgen.2024.100629. Epub 2024 Aug 6.
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.
人类 rDNA 基因座的变异主要是插入缺失（indel）变异。我们开发了一种用于长读段变异calling 的算法，称为 RGA，该算法揭示了数百个 rDNA 拷贝是否具有形成不同类型核糖体的序列变异。我们开发了全长 rRNA 测序（RIBO-RT）和原位测序（SWITCH-seq），结果表明翻译核糖体在 rRNA 中存在变异。超过 1000 个变体的表达水平较低。然而，数十个变体是丰富的，并形成不同的 rRNA 亚型，在插入缺失附近具有不同的结构，如长读段 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/外胚层衍生组织中表现出不同的表达，在癌症中，低丰度的 rRNA 变体可以高度表达。总之，这项研究确定了 rRNA 变体、其染色体位置和独特结构水平的核糖体多样性，以及核糖体变异与组织特异性生物学和癌症的关联。
