Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>

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. T...

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Autores principales:	Nick Panyushev, Larisa Okorokova, Lavrentii Danilov, Leonid Adonin
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	repetitive DNA noncoding RNA mobile elements repetitive elements (REs) transposable elements (transposons TEs) Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d6223c33201f4d1696dd06c522e61f0d
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spelling	oai:doaj.org-article:d6223c33201f4d1696dd06c522e61f0d2021-11-25T16:51:36ZPattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>10.3390/biomedicines91117362227-9059https://doaj.org/article/d6223c33201f4d1696dd06c522e61f0d2021-11-01T00:00:00Zhttps://www.mdpi.com/2227-9059/9/11/1736https://doaj.org/toc/2227-9059Repetitive 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 <i>Strongylocentrotus purpuratus</i>. 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 <i>de novo</i> 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.Nick PanyushevLarisa OkorokovaLavrentii DanilovLeonid AdoninMDPI AGarticlerepetitive DNAnoncoding RNAmobile elementsrepetitive elements (REs)transposable elements (transposonsTEs)Biology (General)QH301-705.5ENBiomedicines, Vol 9, Iss 1736, p 1736 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	repetitive DNA noncoding RNA mobile elements repetitive elements (REs) transposable elements (transposons TEs) Biology (General) QH301-705.5
spellingShingle	repetitive DNA noncoding RNA mobile elements repetitive elements (REs) transposable elements (transposons TEs) Biology (General) QH301-705.5 Nick Panyushev Larisa Okorokova Lavrentii Danilov Leonid Adonin Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
description	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 <i>Strongylocentrotus purpuratus</i>. 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 <i>de novo</i> 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.
format	article
author	Nick Panyushev Larisa Okorokova Lavrentii Danilov Leonid Adonin
author_facet	Nick Panyushev Larisa Okorokova Lavrentii Danilov Leonid Adonin
author_sort	Nick Panyushev
title	Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
title_short	Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
title_full	Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
title_fullStr	Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
title_full_unstemmed	Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>
title_sort	pattern of repetitive element transcription segregate cell lineages during the embryogenesis of sea urchin <i>strongylocentrotus purpuratus</i>
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/d6223c33201f4d1696dd06c522e61f0d
work_keys_str_mv	AT nickpanyushev patternofrepetitiveelementtranscriptionsegregatecelllineagesduringtheembryogenesisofseaurchinistrongylocentrotuspurpuratusi AT larisaokorokova patternofrepetitiveelementtranscriptionsegregatecelllineagesduringtheembryogenesisofseaurchinistrongylocentrotuspurpuratusi AT lavrentiidanilov patternofrepetitiveelementtranscriptionsegregatecelllineagesduringtheembryogenesisofseaurchinistrongylocentrotuspurpuratusi AT leonidadonin patternofrepetitiveelementtranscriptionsegregatecelllineagesduringtheembryogenesisofseaurchinistrongylocentrotuspurpuratusi
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Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin <i>Strongylocentrotus purpuratus</i>

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