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

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

Biomedicines. 2021 Nov 21;9(11):1736. doi: 10.3390/biomedicines9111736.

Authors

Nick Panyushev¹, Larisa Okorokova¹, Lavrentii Danilov², Leonid Adonin^{3

4

5}

Affiliations

¹ Bioinformatics Institute, 197342 St. Petersburg, Russia.
² St. Petersburg State University, Department of Genetics and Biotechnology, 199034 St. Petersburg, Russia.
³ Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
⁴ Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia.
⁵ Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia.

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.

Keywords: TEs); embryogenesis; gastrulation; mobile elements; noncoding RNA; primary mesenchyme cells (PMCs); repetitive DNA; repetitive elements (REs); scRNA-seq; sea urchin Strongylocentrotus purpuratus; transposable elements (transposons.