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

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

PROVIDER: PRJEB9643 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR921729_1.fastq.gz	Fastqsanger.gz
	ERR921729_2.fastq.gz	Fastqsanger.gz
	ERR921730_1.fastq.gz	Fastqsanger.gz
	ERR921730_2.fastq.gz	Fastqsanger.gz
	ERR921731_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

| PRJEB9647 | 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

Rhynchospora breviuscula

Project description:Meiotic recombination dynamics in holocentric Rhynchospora breviuscula

| PRJNA1059790 | 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

A novel algorithm for finding interspersed repeat regions.

Project description:The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together. The complexity of our projection-assemble algorithm is nearly linear to the length of the genome sequence, and its memory usage is limited by the hardware. We tested our algorithm with both simulated data and real biology data, and the results show that our projection-assemble algorithm is efficient. By means of this algorithm, we found an un-labeled repeat region that occurs five times in Escherichia coli genome, with its length more than 5,000 bp, and a mismatch probability less than 4%.

| S-EPMC5172473 | biostudies-literature

SQuIRE reveals locus-specific regulation of interspersed repeat expression.

Project description:Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.

| S-EPMC6411935 | biostudies-literature

Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs).

Project description:Exonization of retroposed mobile elements, a process whereby new exons are generated following changes in non-protein-coding regions of a gene, is thought to have great potential for generating proteins with novel domains. Our previous analysis of primate-specific Alu-short interspersed elements (SINEs) showed, however, that during their 60 million years of evolution, SINE exonizations occurred in some primates, only to be lost again in some of the descendent lineages. This dynamic gain and loss makes it difficult to ascertain the contribution of exonization to genomic novelty. It was speculated that Alu-SINEs are too young to reveal persistent protein exaptation. In the present study we examined older mobile elements, mammalian-wide interspersed repeats (MIRs) that underwent active retroposition prior to the placental mammalian radiation approximately 130 million years ago, to determine their contribution to protein-coding sequences. Of 107 potential cases of MIR exonizations in human, an analysis of splice sites substantiates a mechanism that benefits from 3' splice site selection in MIR sequences. We retraced in detail the evolution of five MIR elements that exonized at different times during mammalian evolution. Four of these are expressed as alternatively spliced transcripts; three in species throughout the mammalian phylogenetic tree and one solely in primates. The fifth is the first experimentally verified, constitutively expressed retroposed SINE element in mammals. This pattern of highly conserved, alternatively and constitutively spliced MIR sequences evinces the potential of exonized transposed elements to evolve beyond the transient state found in Alu-SINEs and persist as important parts of functional proteins.

| S-EPMC1933517 | biostudies-literature

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