Panyushev Nick, Okorokova Larisa, Danilov Lavrentii, Adonin Leonid
Bioinformatics Institute, 197342 St. Petersburg, Russia.
St. Petersburg State University, Department of Genetics and Biotechnology, 199034 St. Petersburg, Russia.
Biomedicines. 2021 Nov 21;9(11):1736. doi: 10.3390/biomedicines9111736.
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of . The most prevalent among these elements were the unknown elements-in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level.
重复元件（REs）占据了真核生物基因组的很大一部分，并在基因组调控中发挥着多种作用。在海胆胚胎发生过程中，大量的重复元件被表达，但这些元件在生物过程调控中的作用仍不清楚。本研究的目的是确定胚胎发生不同阶段的重复元件表达情况。重复元件占[物种名称]基因组DNA的44%。这些元件中最普遍的是未知元件——总体而言，它们占重复元件的78.5%（占基因组总量的35%）。研究发现，在原肠胚形成过程中，基因和重复元件的转录模式发生了显著变化。利用转录组组装，我们表明重复元件的表达与其在基因组中的拷贝数无关。我们还鉴定出了表达的拷贝。在单细胞RNA测序数据中，仅使用活跃的重复元件拷贝进行重复元件表达的定位和定量分析。在所有细胞谱系中均观察到重复元件的表达，并且它们被检测为群体标记。此外，在标记物中，原肠胚间叶细胞（PMC）系的重复元件多样性最大。我们的数据表明，在单细胞分辨率水平上，重复元件在海胆胚胎发生过程中发育域的组织中发挥作用。
