Identification and characterization of centromeric sequences in Xenopus laevis
- Owen K. Smith1,2,
- Charles Limouse1,
- Kelsey A. Fryer1,3,
- Nicole A. Teran3,
- Kousik Sundararajan1,
- Rebecca Heald4 and
- Aaron F. Straight1
- 1Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305-5307, USA;
- 2Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
- 3Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;
- 4Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720-3200, USA
Abstract
Centromeres play an essential function in cell division by specifying the site of kinetochore formation on each chromosome for mitotic spindle attachment. Centromeres are defined epigenetically by the histone H3 variant Centromere Protein A (Cenpa). Cenpa nucleosomes maintain the centromere by designating the site for new Cenpa assembly after dilution by replication. Vertebrate centromeres assemble on tandem arrays of repetitive sequences, but the function of repeat DNA in centromere formation has been challenging to dissect due to the difficulty in manipulating centromeres in cells. Xenopus laevis egg extracts assemble centromeres in vitro, providing a system for studying centromeric DNA functions. However, centromeric sequences in Xenopus laevis have not been extensively characterized. In this study, we combine Cenpa ChIP-seq with a k-mer based analysis approach to identify the Xenopus laevis centromere repeat sequences. By in situ hybridization, we show that Xenopus laevis centromeres contain diverse repeat sequences, and we map the centromere position on each Xenopus laevis chromosome using the distribution of centromere-enriched k-mers. Our identification of Xenopus laevis centromere sequences enables previously unapproachable centromere genomic studies. Our approach should be broadly applicable for the analysis of centromere and other repetitive sequences in any organism.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.267781.120.
- Received June 23, 2020.
- Accepted April 8, 2021.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
