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Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

ABSTRACT: CENH3 ChIP-sequencing (CENH3-ChIPseq) from Rhynchospora pubera leaves

PROVIDER: PRJEB9647 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR922049_1.fastq.gz	Fastqsanger.gz
	ERR922049_2.fastq.gz	Fastqsanger.gz
	ERR922050_1.fastq.gz	Fastqsanger.gz
	ERR922050_2.fastq.gz	Fastqsanger.gz
	ERR922051_1.fastq.gz	Fastqsanger.gz

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Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:BAC sequencing of centromeric regions from Rhynchospora pubera

| PRJEB9649 | ENA

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:Pollen mother cell transcriptome sequencing (RNAseq) from Rhynchospora pubera

| PRJEB9645 | ENA

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:Illumina paired-end HiSeq2000 Sequencing of the genome from Rhynchospora pubera

| PRJEB9643 | ENA

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin.

Project description:Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated "Tyba" and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle-dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.

| S-EPMC4640781 | biostudies-literature

Rhynchospora breviuscula

Project description:Rhynchospora breviuscula overview

| PRJNA1060412 | ENA

ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization

Project description:To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2

2023-05-08 | GSE228407 | GEO

Rhynchospora breviuscula

Project description:Meiotic recombination dynamics in holocentric Rhynchospora breviuscula

| PRJNA1059790 | ENA

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

Project description:We report the binding profile of A. thaliana CENH3, L. oleraceum CENH3 and Z. mays CENH3 in the genetic background of A. thaliana Col ecotype. The L. oleraceum CENH3 and Z. mays CENH3 ChIP was performed in a cenh3 homozygous mutant background expressing CENH3 homologs as transgenes.

2016-10-19 | GSE88907 | GEO

Physcomitrium patens

Project description:Physcomitrium patens CENH3 ChIPseq

| PRJNA1066584 | ENA

Centromere-associated repeat arrays on Trypanosoma brucei chromosomes are much more extensive than predicted.

Project description:BackgroundAfrican trypanosomes belong to a eukaryotic lineage which displays many unusual genetic features. The mechanisms of chromosome segregation in these diploid protozoan parasites are poorly understood. Centromeres in Trypanosoma brucei have been localised to chromosomal regions that contain an array of ~147 bp AT-rich tandem repeats. Initial estimates from the genome sequencing project suggested that these arrays ranged from 2 - 8 kb. In this paper, we show that the centromeric repeat regions are much more extensive.ResultsWe used a long-range restriction endonuclease mapping approach to more accurately define the sizes of the centromeric repeat arrays on the 8 T. brucei chromosomes where unambiguous assembly data were available. The results indicate that the sizes of the arrays on different chromosomes vary from 20 to 120 kb. In addition, we found instances of length heterogeneity between chromosome homologues. For example, values of 20 and 65 kb were obtained for the arrays on chromosome 1, and 50 and 75 kb for chromosome 5.ConclusionsOur results show that centromeric repeat arrays on T. brucei chromosomes are more similar in size to those of higher eukaryotes than previously suspected. This information provides a firmer framework for investigating aspects of chromosome segregation and will allow epigenetic features associated with the process to be more accurately mapped.

| S-EPMC3292466 | biostudies-literature

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