Ontology highlight
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PROVIDER: PRJNA672922 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:We report the sequences bound to CENP-A in the dog genome (Canis familiaris) for high-throughput characterization of centromeric sequences. We compare these ChIPSeq reads (72 bp, single read) against a reference centromeric satellite DNA domain database for the dog genome, resulting in the annotation of sequence variation and estimated abundance of seven satellite families together with adjacent, non-satellite sequences. To study global patterns of sequence diversity and characterizing the subset of sequences correlated with centromere function, these sequences were evaluated relative to a comprehensive centromere sequence domain k-mer library. From this analysis, we identify functional sequence features from two satellite families (CarSat1 and CarSat2) that are defined by distinct arrays subtypes. Sequences bound to CENP-A in MDCK (dog) cell line
2012-07-23 | E-GEOD-38079 | biostudies-arrayexpress
Project description:We report the sequences bound to CENP-A in the dog genome (Canis familiaris) for high-throughput characterization of centromeric sequences. We compare these ChIPSeq reads (72 bp, single read) against a reference centromeric satellite DNA domain database for the dog genome, resulting in the annotation of sequence variation and estimated abundance of seven satellite families together with adjacent, non-satellite sequences. To study global patterns of sequence diversity and characterizing the subset of sequences correlated with centromere function, these sequences were evaluated relative to a comprehensive centromere sequence domain k-mer library. From this analysis, we identify functional sequence features from two satellite families (CarSat1 and CarSat2) that are defined by distinct arrays subtypes.
2012-07-23 | GSE38079 | GEO
Project description:Specification and propagation of the centromeres of eukaryotic chromosomes is determined by epigenetic mechanisms. Unfortunately, the epigenetic characteristics of centromeric DNA and chromatin are difficult to define because the centromeres are composed of highly repetitive DNA sequences in most eukaryotic species. Several rice centromeres have been fully sequenced, making rice an excellent model for centromere research. We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The DNA sequences in the core domains of rice Cen4, Cen5, and Cen8 showed elevated methylation levels compared to the sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains compared to the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared to the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin. mCIP-seq of one sample of rice seedling
2010-04-22 | E-GEOD-21414 | biostudies-arrayexpress
Project description:CUT&RUN experiment was carried out on bovine semeimbranosous muscle satellite cells to identify the locus of the accumulation of the centromeric protein A (CENP-A) on the cattle Y-chromosome. This was carried out to support the annotation of the DNA signal comprising tandem array of a centromeric satellite signal which characterizes the centromere on the Y-chromosome.
2024-10-02 | GSE262830 | GEO
Project description:We report that DNA2 predominantly bound to the centromeric α-satellite regions. The centromeric regions contained 58% of the DNA2-associated DNA, representing a 33.5-fold enrichment over genomic input. To define the under-replicated DNA regions in DNA2-null cells, we conducted whole-genome DNA sequencing of the under-replicated BrdU negative DNA. After normalization to genomic input DNA from the same cells, 12.9% of the peaks from the under-replicated DNA aligned with the centromeric DNA regions, representing an 8.5-fold enrichment. In addition, among the peaks that overlapped between the DNA2 pull-down and under-replicated regions, two thirds fell into the centromeric regions, representing a 48-fold enrichment.
2018-04-10 | GSE108619 | GEO
Project description:CDCA7, encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of peri/centromeric satellite DNA. Previous work suggests that the CDCA7 CRD is implicated in DNA binding, which plays a key role in directing the DNA methylation mechinery to peri/centromeric regions. To identify potential genomic targets of CDCA7, we performed ChIP-Seq using CDCA7 knockout (KO) mouse embryonic stem cells (mESCs) stably expressing HA-tagged wild-type (WT) or ICF mutant (R285H) mCDCA7.
2024-07-31 | GSE255395 | GEO
Project description:The biorientation of sister chromatids on the mitotic spindle, essential for accurate sister chromatid segregation, relies on critical centromere components including cohesin, the centromere-specific H3 variant CENP-A, and centromeric DNA. Centromeric DNA is highly variable between chromosomes yet must accomplish a similar function. Moreover, how the 50 nm cohesin ring, proposed to encircle sister chromatids, accommodates inter-sister centromeric distances of hundreds of nanometers on the metaphase spindle is a conundrum. Insight into the 3D organization of centromere components would help resolve how centromeres function on the mitotic spindle. We used ChIP-seq and super-resolution microscopy to examine the geometry of essential centromeric components on human chromosomes. ChIP-seq of SA1, SA2, and Rad21 in human cells demonstrates that cohesin subunits are depleted in -satellite arrays where CENP-A nucleosomes and kinetochores assemble. Cohesin is instead enriched at pericentromeric DNA. Structured illumination microscopy of sister centromeres is consistent, revealing a non-overlapping pattern of CENP-A and cohesin.
2023-10-11 | GSE240957 | GEO
Project description:We used native ChIP-seq of CENP-A-containing particles from normal centromeres on alpha-satellite DNA and three naturally-occurring neocentromeres to test the proposed models for the major form of the fundamental repeating unit of centromeric chromatin. We found that the predominant form of the CENP-A particle at the centromere is an octameric nucleosome with loose terminal DNA. Additionally, we found CENP-A nucleosomes are strongly phased on the 171 bp alpha-satellite monomers of normal centromeres, and also display strong positioning and neocentromeres. Comparison of CENP-A and bulk nucleosome DNA lengths and positions in three different human neocentromere-containing cell lines
2013-05-04 | E-GEOD-44724 | biostudies-arrayexpress
Project description:BAC sequencing of centromeric regions from Rhynchospora pubera
| PRJEB9649 | ENA