Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization

ABSTRACT: To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE145600 | GEO | 2021/08/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification and characterization of centromeric sequences in Xenopus laevis

Project description:Centromeres play an essential role in cell division by specifying the site of kinetochore formation on each chromosome so that chromosomes can attach to the mitotic spindle for segregation. Centromeres are defined epigenetically by the histone H3 variant CEntromere Protein A (CENP-A). Dividing cells maintain the centromere by depositing new CENP-A each cell cycle to replenish CENP-A diluted by replication. The CENP-A nucleosome serves as the primary signal to the machinery responsible for its replenishment. Vertebrate centromeres are frequently built on repetitive sequences organized in tandem arrays. Repetitive centromeric DNA has been suggested to play a role in centromere maintenance and in de novo centromere formation, but this has been difficult to dissect because of the difficulty in manipulating centromere in cells. Extracts from Xenopus laevis eggs are able to assemble centromeres and kinetochores in vitro and thus provide a useful system for studying the role of centromeric DNA in centromere formation. However centromeric sequences in X. laevis have not been extensively characterized.. In this study we characterize repeat sequences found at X. laevis centromeres. We utilize a k-mer based approach in order to uncover the previously unknown diversity of X. laevis centromeric sequences. We validate centromere localization of repeat sequences by in situ hybridization and identify the location of the centromeric repetitive array on each chromosome by mapping the distribution of centromere enriched k-mers on the Xenopus genome. Our identification of X. laevis centromere sequences enables previously unapproachable genomic studies of centromeres. The k-mer based approach that we used to investigate centromeric repetitive DNA is suitable for the analysis of other repetitive sequences found across the genome or the study of repeats in other organisms.

2020-06-24 | GSE153058 | GEO

Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 3)

Project description:Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes. Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences such as human alpha satellite arrays. Such analyses suggest that properties of centromeric DNA itself may favour assembly of CENP-A rather than H3 nucleosomes. To investigate the innate properties of centromeric DNA we have examined histone dynamics on this DNA assembled in CENP-A chromatin at endogenous centromeres and when assembled only in H3 chromatin at an ectopic location. We demonstrate that H3 occupancy on centromeric DNA is innately low while H3 turnover is high. Moreover, even at an ectopic location centromeric DNA programs H3 deposition in S phase and its eviction during G2 when CENP-A is otherwise deposited. G2 accumulation of RNAPII on centromeric DNA during G2 is consistent with transcription-coupled destabilisation of H3 nucleosomes to favour CENP-A deposition.

2018-11-29 | GSE119922 | GEO

Fission yeasts CENPA and H3K9me Chip-seq

2019-03-04 | GSE112454 | GEO

Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 1)

2018-11-29 | GSE106491 | GEO

Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 2)

2018-11-29 | GSE106492 | GEO

Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [ChIP-seq]

Project description: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.

2021-05-24 | GSE161308 | GEO

Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [RNA-seq]

2021-05-24 | GSE161191 | GEO

Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells

Project description:Although apoptotic cells (ACs) contain nucleic acids that can be recognized by Toll-like receptors (TLRs), engulfment of ACs does not initiate inflammation in healthy organisms. To better understand this phenomenon, we identified and characterized macrophage populations that continually engulf ACs in several distinct tissues. These macrophages share characteristics compatible with immunologically silent clearance of ACs, including high expression of AC recognition receptors, low expression of TLR9, and reduced TLR responsiveness to nucleic acids. When removed from tissues, these macrophages lose many of these characteristics and generate inflammatory responses to AC-derived nucleic acids, suggesting that cues from the tissue microenvironment are required to program macrophages for silent AC clearance. We show that KLF2 and KLF4 control expression of many genes within this AC clearance program. Coordinated expression of AC receptors with genes that limit responses to nucleic acids may represent a central feature of tissue macrophages that ensures maintenance of homeostasis.

2017-11-15 | GSE93820 | GEO

Transcriptome sequencing at early stage infection of the wheat pathogen Zymoseptoria tritici reveals chromosomal differences in transcription patterns and host specific gene expression.

Project description:We have applied whole transcriptome profiling to infer genetic determinants of pathogenicity and host specialization in Z. tritici. Our data includes RNAseq data from early infection stages of a compatible (wheat) and a non-compatible host (Brachypodium distachyon). Overall transcription of AC genes is remarkably lower than genes on core chromosomes (CC) and only 40% of the genes are transcribed. We identify 31 AC and 1069 CC genes showing plant specific expression. In addition 21 CC genes are only upregulated in wheat supporting functional relevance in host specificity. We further explore the genomic composition and distribution of unique and paralogous genes in Z. tritici focusing on the evolutionary origin of AC genes. In contrast to previous studies we show that ACs mainly encode unique genes. Phylogenetic analyses suggest that rare duplication events in the Z. tritici genome precede diversification of Zymoseptoria species and demonstrate that ACs have been maintained in the genome of Zymoseptoria over long evolutionary times.

2014-06-30 | GSE54874 | GEO

Transcriptome sequencing at early stage infection of the wheat pathogen Zymoseptoria tritici reveals chromosomal differences in transcription patterns and host specific gene expression.

2014-06-30 | E-GEOD-54874 | biostudies-arrayexpress