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| Status |
Public on May 24, 2021 |
| Title |
Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [RNA-seq] |
| Organisms |
Symphalangus syndactylus; Nomascus leucogenys; Hylobates moloch; Hoolock leuconedys |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.
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| Overall design |
Total RNA-sequencing was carried out on four gibbon species, representing the four extant gibbon genera (Siamang, Hylobates, Hoolock and Nomascus).
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| Contributor(s) |
Hartley G, Okhovat M, O'Neill R, Carbone L |
| Citation(s) |
33983366, 36146896 |
| BioProject |
PRJNA666911 |
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| Submission date |
Nov 10, 2020 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
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| Department |
Medicine
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| Street address |
3030 S Moody Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platforms (4)
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| GPL25055 |
Illumina NextSeq 500 (Nomascus leucogenys) |
| GPL29392 |
Illumina NextSeq 500 (Hoolock leuconedys) |
| GPL29393 |
Illumina NextSeq 500 (Symphalangus syndactylus) |
| GPL29394 |
Illumina NextSeq 500 (Hylobates moloch) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE161217 |
Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE161191_RAW.tar |
700.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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