Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1091572 | ENA |
REPOSITORIES: ENA
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Project description:Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T-CHM13) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to T2T-CHM13 identified highly similar CENP-A position following multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and site of kinetochore recruitment varies among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained at their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.
2023-01-01 | GSE221541 | GEO
Project description:The haplotype 2 of T2T genome for Wolley grape
| PRJNA1130656 | ENA
Project description:The haplotype 1 of T2T genome for Wolley grape
| PRJNA1130655 | ENA
Project description:During ripening of fruits stored under low temperatures, a number of physiological alterations which are manifested in a reduction of juice content take place, resulting in the apparition of woolly fruits. Modifications in cell wall structure during the ripening process are proposed to be key to determine the decreasing of juice content in woolly fruits. Under the assumption that changes in relative abundance of genes related to cell wall metabolism would be involved in woolliness development, in this work we present an analysis of the expression of multiple genes, which serves as an approximation to uncover the mechanisms behind this physiological alteration. The expression of 847 genes was examined using macroarrays hybridizations. Membranes were hybridized with 32P-labeled cDNAs synthesized from mRNAs of juice and woolly peaches. The results showed that 67.5% of the clones (n = 573) fulfilled all filter criteria and they were selected for sequence analysis. Our analysis indicate that 45% of transcripts which present a consistent expression level in all biological replicates are activated exclusively in juice condition, and only 15% in woolly fruits. In the resting 40% (transcripts common to both conditions,) only 5% presents an abundance increase in woolly samples. Keywords: Analysis of physiological disorder in peaches
2007-04-30 | GSE7145 | GEO
Project description:The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.
2024-12-29 | PXD050500 | Pride
Project description:Recent completion of the telomere-to-telomere (T2T) genome assembly has enabled a comprehensive characterization of pericentromeric SatⅠ, SatII, SatⅢ and centromeric α-satellite repeats. SatⅢ DNA constitutes ~1.56% of the genome with a reported localization across 16 chromosomes. The transcription activity of SatⅢ DNA across genome and the sequence of SatⅢ transcripts remained largely unclear. We performed nanopore long-read RNA sequencing (RNA-seq) in untreated (UN), sodium arsenite (SA: 0.1mM, 5 h) and heat shock (HS: 42°C, 2 h; 37°C, 1 h) stressed HeLa cells to characterize SatⅢ transcripts . Since a portion of SatⅢ transcripts is non-polyadenylated, We performed polyadenylated (poly(A)+) and rRNA-depleted (ribo-) nanopore cDNA long-read RNA-seq.
2025-05-26 | GSE277764 | GEO