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Genome Res
2021 Jun 01;316:958-967. doi: 10.1101/gr.267781.120.
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Identification and characterization of centromeric sequences in Xenopus laevis.
Smith OK
,
Limouse C
,
Fryer KA
,
Teran NA
,
Sundararajan K
,
Heald R
,
Straight AF
.
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.
Akiyoshi,
Tension directly stabilizes reconstituted kinetochore-microtubule attachments.
2010,
Pubmed
Benson,
Tandem repeats finder: a program to analyze DNA sequences.
1999,
Pubmed
Desai,
A method that allows the assembly of kinetochore components onto chromosomes condensed in clarified Xenopus egg extracts.
1997,
Pubmed
,
Xenbase
Edwards,
Identification of xenopus CENP-A and an associated centromeric DNA repeat.
2005,
Pubmed
,
Xenbase
Foley,
Microtubule attachment and spindle assembly checkpoint signalling at the kinetochore.
2013,
Pubmed
French,
Xenopus laevis M18BP1 Directly Binds Existing CENP-A Nucleosomes to Promote Centromeric Chromatin Assembly.
2017,
Pubmed
,
Xenbase
Fu,
CD-HIT: accelerated for clustering the next-generation sequencing data.
2012,
Pubmed
Grant,
FIMO: scanning for occurrences of a given motif.
2011,
Pubmed
Guse,
In vitro centromere and kinetochore assembly on defined chromatin templates.
2011,
Pubmed
,
Xenbase
Harrington,
Formation of de novo centromeres and construction of first-generation human artificial microchromosomes.
1997,
Pubmed
Hayden,
Composition and organization of active centromere sequences in complex genomes.
2012,
Pubmed
Hayden,
Sequences associated with centromere competency in the human genome.
2013,
Pubmed
Heger,
GAT: a simulation framework for testing the association of genomic intervals.
2013,
Pubmed
Hyman,
Microtubule-motor activity of a yeast centromere-binding protein complex.
1992,
Pubmed
Kasinathan,
Non-B-Form DNA Is Enriched at Centromeres.
2018,
Pubmed
Kokot,
KMC 3: counting and manipulating k-mer statistics.
2017,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed
Logsdon,
Human Artificial Chromosomes that Bypass Centromeric DNA.
2019,
Pubmed
Manuelidis,
Complex and simple sequences in human repeated DNAs.
1978,
Pubmed
McDermid,
Isolation and characterization of an alpha-satellite repeated sequence from human chromosome 22.
1986,
Pubmed
McNulty,
Alpha satellite DNA biology: finding function in the recesses of the genome.
2018,
Pubmed
Melters,
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
2013,
Pubmed
Miga,
Centromere reference models for human chromosomes X and Y satellite arrays.
2014,
Pubmed
Milks,
Dissection of CENP-C-directed centromere and kinetochore assembly.
2009,
Pubmed
,
Xenbase
Moree,
CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly.
2011,
Pubmed
,
Xenbase
Musacchio,
A Molecular View of Kinetochore Assembly and Function.
2017,
Pubmed
Ng,
Mutational and in vitro protein-binding studies on centromere DNA from Saccharomyces cerevisiae.
1987,
Pubmed
Ngan,
The centromere enhancer mediates centromere activation in Schizosaccharomyces pombe.
1997,
Pubmed
Ohzeki,
CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA.
2002,
Pubmed
Ohzeki,
Genetic and epigenetic regulation of centromeres: a look at HAC formation.
2015,
Pubmed
Peacock,
The organization of highly repeated DNA sequences in Drosophila melanogaster chromosomes.
1974,
Pubmed
Ramírez,
deepTools2: a next generation web server for deep-sequencing data analysis.
2016,
Pubmed
Ramírez,
High-resolution TADs reveal DNA sequences underlying genome organization in flies.
2018,
Pubmed
Rudd,
Sequence organization and functional annotation of human centromeres.
2003,
Pubmed
Seibt,
FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses.
2018,
Pubmed
Session,
Genome evolution in the allotetraploid frog Xenopus laevis.
2016,
Pubmed
,
Xenbase
Sorger,
Factors required for the binding of reassembled yeast kinetochores to microtubules in vitro.
1994,
Pubmed
Sullivan,
Genomic size of CENP-A domain is proportional to total alpha satellite array size at human centromeres and expands in cancer cells.
2011,
Pubmed
Sullivan,
α satellite DNA variation and function of the human centromere.
2017,
Pubmed
Sun,
Molecular structure of a functional Drosophila centromere.
1997,
Pubmed
Sun,
Sequence analysis of a functional Drosophila centromere.
2003,
Pubmed
Zasadzińska,
Orchestrating the Specific Assembly of Centromeric Nucleosomes.
2017,
Pubmed