Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus.

Nick Panyushev,Larisa Okorokova,Lavrentii Danilov,Leonid Adonin

doi:10.3390/biomedicines9111736

Abstract

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 Strongylocentrotus purpuratus. 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 de novo 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.

Highlights

Eukaryotic genomes are larger and more complex than those of prokaryotes, and they significantly differ in size
In an in-depth analysis of sequences of eukaryotic genomes, it became clear that the differences in genome size are due to the presence of different amounts of repetitive DNA, while the number of functional genes varies within the same range [5]
The presence of repetitive DNA is a distinctive feature of eukaryotic genomes; it occupies a major part of the overall nuclear DNA

Summary

Introduction

Eukaryotic genomes are larger and more complex than those of prokaryotes, and they significantly differ in size. There is no correlation between the genome size and the organism complexity. In an in-depth analysis of sequences of eukaryotic genomes, it became clear that the differences in genome size are due to the presence of different amounts of repetitive DNA, while the number of functional genes varies within the same range (up to 25,000) [5]. This phenomenon was described by Waring and Britten a half-century ago using reassociation studies [6,7]. The presence of repetitive DNA is a distinctive feature of eukaryotic genomes; it occupies a major part of the overall nuclear DNA

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