Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas
Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is...
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ftrboskovicinst:oai:fulir.irb.hr:6107 2023-05-15T15:58:08+02:00 Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas Tunjić Cvitanić, Monika Vojvoda Zeljko, Tanja Pasantes, Juan J. García-Souto, Daniel Gržan, Tena Despot-Slade, Evelin Plohl, Miroslav Šatović, Eva 2020 application/pdf http://fulir.irb.hr/6107/ http://fulir.irb.hr/6107/1/genes-11-00695-v2.pdf https://www.mdpi.com/2073-4425/11/6/695 https://doi.org/10.3390/genes11060695 en eng MDPI info:eu-repo/grantAgreement/HRZZ/IP/IP-2014-09-3183 http://fulir.irb.hr/6107/ https://www.mdpi.com/2073-4425/11/6/695 doi:10.3390/genes11060695 http://fulir.irb.hr/6107/1/genes-11-00695-v2.pdf info:eu-repo/semantics/openAccess Genes Biology info:eu-repo/semantics/article 2020 ftrboskovicinst https://doi.org/10.3390/genes11060695 2022-07-08T13:11:05Z Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Ruđer Bošković Institute Zagreb: Full-text Institutional Repository (FULIR) Pacific Genes 11 6 695 |
institution |
Open Polar |
collection |
Ruđer Bošković Institute Zagreb: Full-text Institutional Repository (FULIR) |
op_collection_id |
ftrboskovicinst |
language |
English |
topic |
Biology |
spellingShingle |
Biology Tunjić Cvitanić, Monika Vojvoda Zeljko, Tanja Pasantes, Juan J. García-Souto, Daniel Gržan, Tena Despot-Slade, Evelin Plohl, Miroslav Šatović, Eva Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
topic_facet |
Biology |
description |
Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons. |
format |
Article in Journal/Newspaper |
author |
Tunjić Cvitanić, Monika Vojvoda Zeljko, Tanja Pasantes, Juan J. García-Souto, Daniel Gržan, Tena Despot-Slade, Evelin Plohl, Miroslav Šatović, Eva |
author_facet |
Tunjić Cvitanić, Monika Vojvoda Zeljko, Tanja Pasantes, Juan J. García-Souto, Daniel Gržan, Tena Despot-Slade, Evelin Plohl, Miroslav Šatović, Eva |
author_sort |
Tunjić Cvitanić, Monika |
title |
Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
title_short |
Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
title_full |
Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
title_fullStr |
Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
title_full_unstemmed |
Sequence composition underlying centromeric and heterochromatic genome compartments of the Pacific oyster Crassostrea gigas |
title_sort |
sequence composition underlying centromeric and heterochromatic genome compartments of the pacific oyster crassostrea gigas |
publisher |
MDPI |
publishDate |
2020 |
url |
http://fulir.irb.hr/6107/ http://fulir.irb.hr/6107/1/genes-11-00695-v2.pdf https://www.mdpi.com/2073-4425/11/6/695 https://doi.org/10.3390/genes11060695 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Genes |
op_relation |
info:eu-repo/grantAgreement/HRZZ/IP/IP-2014-09-3183 http://fulir.irb.hr/6107/ https://www.mdpi.com/2073-4425/11/6/695 doi:10.3390/genes11060695 http://fulir.irb.hr/6107/1/genes-11-00695-v2.pdf |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3390/genes11060695 |
container_title |
Genes |
container_volume |
11 |
container_issue |
6 |
container_start_page |
695 |
_version_ |
1766393852511387648 |