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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ftmdpi:oai:mdpi.com:/2073-4425/11/6/695/ 2023-08-20T04:06:01+02:00 Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas Monika Tunjić Cvitanić Tanja Vojvoda Zeljko Juan J. Pasantes Daniel García-Souto Tena Gržan Evelin Despot-Slade Miroslav Plohl Eva Šatović agris 2020-06-24 application/pdf https://doi.org/10.3390/genes11060695 EN eng Multidisciplinary Digital Publishing Institute Animal Genetics and Genomics https://dx.doi.org/10.3390/genes11060695 https://creativecommons.org/licenses/by/4.0/ Genes; Volume 11; Issue 6; Pages: 695 centromere CenH3 heterochromatin H3K9me3 chromatin immunoprecipitation repetitive DNA Bivalves Crassostrea gigas Text 2020 ftmdpi https://doi.org/10.3390/genes11060695 2023-07-31T23:41:02Z 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. Text Crassostrea gigas Pacific oyster MDPI Open Access Publishing Pacific Genes 11 6 695 |
institution |
Open Polar |
collection |
MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
centromere CenH3 heterochromatin H3K9me3 chromatin immunoprecipitation repetitive DNA Bivalves Crassostrea gigas |
spellingShingle |
centromere CenH3 heterochromatin H3K9me3 chromatin immunoprecipitation repetitive DNA Bivalves Crassostrea gigas Monika Tunjić Cvitanić Tanja Vojvoda Zeljko Juan J. Pasantes Daniel García-Souto Tena Gržan Evelin Despot-Slade Miroslav Plohl Eva Šatović Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas |
topic_facet |
centromere CenH3 heterochromatin H3K9me3 chromatin immunoprecipitation repetitive DNA Bivalves Crassostrea gigas |
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 |
Text |
author |
Monika Tunjić Cvitanić Tanja Vojvoda Zeljko Juan J. Pasantes Daniel García-Souto Tena Gržan Evelin Despot-Slade Miroslav Plohl Eva Šatović |
author_facet |
Monika Tunjić Cvitanić Tanja Vojvoda Zeljko Juan J. Pasantes Daniel García-Souto Tena Gržan Evelin Despot-Slade Miroslav Plohl Eva Šatović |
author_sort |
Monika Tunjić Cvitanić |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2020 |
url |
https://doi.org/10.3390/genes11060695 |
op_coverage |
agris |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Genes; Volume 11; Issue 6; Pages: 695 |
op_relation |
Animal Genetics and Genomics https://dx.doi.org/10.3390/genes11060695 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/genes11060695 |
container_title |
Genes |
container_volume |
11 |
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6 |
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695 |
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1774716923265679360 |