Centromere evolution in Oryza genus
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ABSTRACT:
PROVIDER: PRJEB27372 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.
2016-04-02 | GSE63752 | GEO
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).
2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress
Project description:Centromeric repetitive DNA sequences are highly variable during evolution, which are the hub for genome stability in almost all the eukaryotic organisms. However, how centromeric repeat sequences diverge rapidly among closely related species and populations, and how polyploidy contributed to the diversity of centromere among co-evolved subgenomes are largely unknown. Here, we applied the Brachypodium system to investigate the track of centromere evolution within this taxa, and their adaptation to alloploidization process. Subgenome divergent centromeric satellite repeat were discovered in tetraploid B. hybridum, and this divergent was originated form their two diploid progenitors. Furthermore, differential sequences influence the association sites with CENH3 nucleosomes on the monomer satellite repeats, and positioning of CENH3 nucleosomes on the satellite DNA are stable in each subgenome after alloploidization. Only minor intrasubgenomic variations were observed on these satellite repeats from diploid to tetraploid in B. hybridum, and no evident intersubgenomic transfer of centromeric satellite repeats after alloploidization. Pan-genome analysis reveals that the general principle of centromere dynamic within the populations in Brachypodium genomes with different polyploidy level. Our results provide an unprecedented information regarding the genomic and functional diversity of centromeric repeat DNA during evolution.
2022-12-01 | GSE157143 | GEO
Project description:CENP-A is the histone H3 variant necessary to specify the location of all eukaryoticcentromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7,has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viability. Thus, we conclude that phosphorylation of CENP-A on serine 7 is dispensable to maintain correct centromere dynamics and function.
2019-01-28 | PXD012163 | Pride
Project description:cotton centromere study using ChIP-seq
| PRJEB14368 | ENA
Project description:We conduct a genome-wide analysis of the DNA sequences associated with CenH3 using chromatin immunoprecipitation to map the position of centromere regions.
2019-01-17 | GSE119184 | GEO
Project description:Centromere repositioning in Schizosaccharomyces pombe
| PRJNA484011 | ENA
Project description:We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of both mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2 in fission yeast. We find that neocemtromeres are formed preferably at pericentromeric regions in single depletion of CENP-T-W-X-S.
2019-09-28 | GSE117955 | GEO
Project description:De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Derivative 3-3 contains a de novo centromere, which was derived from a euchromatic site on the short arm of chromosome 9 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 288 kb with a high-density gene distribution with low-density of transposons. Here we applied next generation sequencing technology to analyze gene transcription, DNA methylation for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences.
2016-08-05 | GSE76533 | GEO