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Xenopus laevis

ABSTRACT: Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis

PROVIDER: PRJNA300520 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2858152_1.fastq.gz	Fastqsanger.gz
	SRR2858152_2.fastq.gz	Fastqsanger.gz
	SRR2858153_1.fastq.gz	Fastqsanger.gz
	SRR2858153_2.fastq.gz	Fastqsanger.gz
	SRR2858154_1.fastq.gz	Fastqsanger.gz

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Project description:We implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. Gene expression analysis of Xenopus laevis juvenile inner ear tissue. Inner ear RNA isolated from three groups of 5-10 juvenile X. laevis. Each biological replicate represents pooled inner ear RNA from 10-19 inner ears.

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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.

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