Structure and Evolution of Plant Centromeres

Nagaki, Kiyotaka; Walling, Jason G.; Hirsch, Cory D.; Jiang, Jiming; Murata, Minoru

doi:10.1007/978-3-642-00182-6_6

Cited by 13 publications

(10 citation statements)

References 168 publications

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“…These sequences are not necessarily restricted to centromeric regions, as has been shown in multiple organisms (Sun et al 1997;Rudd and Willard 2004;Ma et al 2007;Cellamare et al 2009;Nagaki et al 2009;Shang et al 2010). This observation begs the question of what is the possible role of such sequences away from their centromeric home.…”

Section: Resurrectionmentioning

confidence: 70%

The evolutionary life cycle of the resilient centromere

Kalitsis

Choo

2012

Chromosoma

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The centromere is a chromosomal structure that is essential for the accurate segregation of replicated eukaryotic chromosomes to daughter cells. In most centromeres, the underlying DNA is principally made up of repetitive DNA elements, such as tandemly repeated satellite DNA and retrotransposable elements. Paradoxically, for such an essential genomic region, the DNA is rapidly evolving both within and between species. In this review, we show that the centromere locus is a resilient structure that can undergo evolutionary cycles of birth, growth, maturity, death and resurrection. The birth phase is highlighted by examples in humans and other organisms where centromere DNA deletions or chromosome rearrangements can trigger the epigenetic assembly of neocentromeres onto genomic sites without typical features of centromere DNA. In addition, functional centromeres can be generated in the laboratory using various methodologies. Recent mapping of the foundation centromere mark, the histone H3 variant CENP-A, onto near-complete genomes has uncovered examples of new centromeres which have not accumulated centromere repeat DNA. During the growth period of the centromere, repeat DNA begins to appear at some, but not all, loci. The maturity stage is characterised by centromere repeat accumulation, expansions and contractions and the rapid evolution of the centromere DNA between chromosomes of the same species and between species. This stage provides inherent centromere stability, facilitated by repression of gene activity and meiotic recombination at and around the centromeres. Death to a centromere can result from genomic instability precipitating rearrangements, deletions, accumulation of mutations and the loss of essential centromere binding proteins. Surprisingly, ancestral centromeres can undergo resurrection either in the field or in the laboratory, via as yet poorly understood mechanisms. The underlying principle for the preservation of a centromeric evolutionary life cycle is to provide resilience and perpetuity for the all-important structure and function of the centromere.

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Section: Resurrectionmentioning

confidence: 70%

The evolutionary life cycle of the resilient centromere

Kalitsis

Choo

2012

Chromosoma

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“…As the case, though comparison of the HaloTag system and other established methods makes better evidence, the HaloTag system is able to supply an easy isolation method for centromeric DNA. Generally, all centromeres of an organism are composed of a single type of tandem-repeat or micro-satellite DNA (Choo 1997;Murata 2002;Jiang et al 2003;Nagaki et al 2009b). Based on these findings, the selection and homogenization of centromeric DNA sequences by a mutated CENH3 has been hypothesized (Henikoff et al 2001).…”

Section: Discussionmentioning

confidence: 99%

“…Among these centromere-specific proteins, a centromere-specific histone H3 variant, CENH3, was first identified as CENP-A from antigens in autoimmune disease patients (Earnshaw and Rothfield 1985). Its orthologs have been identified in all eukaryotic species studied, and are recognized as a key component for recruiting other centromeric proteins (Henikoff et al 2001;Fukagawa 2004;Nagaki et al 2009b). Their localization is a good indicator of centromere activity because CENH3s localize only on functional centromeres (Warburton et al 1997;Nasuda et al 2005;Han et al 2006).…”

Section: Introductionmentioning

confidence: 98%

“…Despite the importance of centromere functions among eukaryotes, centromeric DNA sequences are not well conserved even among related species (Choo 1997;Murata 2002;Jiang et al 2003;Nagaki et al 2009b). The centromeres of multicellular eukaryotes are usually composed of a long array of tandem repeated DNA sequences or microsatellites.…”

Section: Introductionmentioning

confidence: 99%

“…CENH3 is composed of a species-specific aminotail and a conserved histone fold domain (HFD). Since amino acid sequences of the amino-tails are so divergent, it is difficult to raise an antibody that recognizes all CENH3 (Henikoff et al 2001;Nagaki et al 2009b). On the other hand, HFD is not an appropriate region as an antigen because the amino acid sequences are similar to that of canonical histone H3, and it is packed into a nucleosome.…”

Section: Introductionmentioning

confidence: 99%

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Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco

et al. 2011

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The centromere is a multi-functional complex comprising centromeric DNA and a number of proteins. To isolate unidentified centromeric DNA sequences, centromere-specific histone H3 variants (CENH3) and chromatin immunoprecipitation (ChIP) have been utilized in some plant species. However, anti-CENH3 antibody for ChIP must be raised in each species because of its species specificity. Production of the antibodies is time-consuming and costly, and it is not easy to produce ChIP-grade antibodies. In this study, we applied a HaloTag7-based chromatin affinity purification system to isolate centromeric DNA sequences in tobacco. This system required no specific antibody, and made it possible to apply a highly stringent wash to remove contaminated DNA. As a result, we succeeded in isolating five tandem repetitive DNA sequences in addition to the centromeric retrotransposons that were previously identified by ChIP. Three of the tandem repeats were centromere-specific sequences located on different chromosomes. These results confirm the validity of the HaloTag7-based chromatin affinity purification system as an alternative method to ChIP for isolating unknown centromeric DNA sequences. The discovery of more than two chromosome-specific centromeric DNA sequences indicates the mosaic structure of tobacco centromeres.

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