Panyushev N et al. (2021), Pattern of Repetitive Element Transcription Seg...

ECB-ART-50663

Biomedicines 2021 Nov 21;911:. doi: 10.3390/biomedicines9111736.

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

Panyushev N , Okorokova L , Danilov L , Adonin L .

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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.

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	Figure 1. Donut plot of repetitive sequences in the genome of Strongylocentrotus purpuratus, version 5.0. The inner circle corresponds to the type of REs, the outer to the REs family.
	Figure 2. Interspersed repeat landscape in the Strongylocentrotus purpuratus genome. TE classes are marked with colors: SINEs, blue; LINE, red; LTR TE, yellow; DNA transposons, green; non-annotated repeats, brown.
	Figure 3. RE expression significantly changes during the gastrulation process irrespective of their origin and number of copies. Volcano plot showing differential expression of gene-coding transcripts (a) and RE (b) between blastula and gastrula stages. Each transcript is shown as a single point. Those with significantly changed levels are orange; black points are those without significant changes in transcription. (c) Scatter plot of expressed repetitive elements. X-axis represents the copy number of a given RE in the genome. Y-axis represents the number of transcribed copies of this element. Color gradient from blue to red indicates the length of the element. RE families with the length > 500 bp are shown with cyan dots. (d) Heat map of repetitive elements transcription that are differentially expressed during the gastrulation by embryo stages. Type column denotes the RE type. Class row denotes the embryo stage. Top 500 elements by their logFC were selected for this plot.
	Figure 4. Results of the single-cell RNA-seq analysis. Umap plots of each embryo stage separately. (a) 64-cell embryo; (b) morula stage; (c) hatched blastula; (d) mesenchyme blastula; (e) early gastrula; (f) late gastrula.
	Figure 5. Feature plot of 64—cell stage. Cluster 0 corresponds to the vegetal pole of the embryo, cluster 1 to the vegetal pole. Each point corresponds to the single cell, and its color marks the level of either H1 (a) or SpAN (b) gene expression.
	Figure 6. Results of the single-cell RNA-seq analysis. Dot plot of the expression of cell populations markers and REs. From left to right: ARS to MTa—aboral ectoderm markers; COLP4alpha to SM50—PMC markers (marked in pink); NK2.1 to Hlf—apical plate markers; blimp1/krox to LOC115921637—endoderm markers; Lefty to LOC575348—oral ectoderm markers; Cyclophilin to GATAc—markers of SMC; Aura to Kozhim—novel REs.

References [+] :

Adonin, Sea Urchin as a Universal Model for Studies of Gene Networks. 2020, Pubmed, Echinobase