Sequencing of a rice centromere uncovers active genes

Nagaki, Kiyotaka; Cheng, Zhukuan; Ouyang, Shuai; Talbert, Paul B.; Kim, Mary; Jones, Kristine; Henikoff, Steven; Buell, C. Robin; Jiang, Jiming

doi:10.1038/ng1289

Cited by 487 publications

(554 citation statements)

References 49 publications

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“…A more recent study has shown that centrochromatin has a histone modification pattern resembling that found in the downstream body of transcribed genes (Bergmann et al, 2011). Indeed, previous studies have detected transcription within rice centromeres (Nagaki et al, 2004), human neocentromeres (Saffery et al, 2003) and also within the alphoid array of a derivative of the synthetic HAC used in the present study (Iida et al, 2010). The chromatin profile at active kinetochores resembles the 'yellow' chromatin described in a recent paper (Filion et al, 2010).…”

Section: Discussionmentioning

confidence: 58%

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

Bergmann

Jakubsche

Martins

et al. 2012

Journal of Cell Science

102

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SummaryHuman kinetochores are transcriptionally active, producing very low levels of transcripts of the underlying alpha-satellite DNA. However, it is not known whether kinetochores can tolerate acetylated chromatin and the levels of transcription that are characteristic of housekeeping genes, or whether kinetochore-associated 'centrochromatin', despite being transcribed at a low level, is essentially a form of repressive chromatin. Here, we have engineered two types of acetylated chromatin within the centromere of a synthetic human artificial chromosome. Tethering a minimal NF-kB p65 activation domain within kinetochore-associated chromatin produced chromatin with high levels of histone H3 acetylated on lysine 9 (H3K9ac) and an ,10-fold elevation in transcript levels, but had no substantial effect on kinetochore assembly or function. By contrast, tethering the herpes virus VP16 activation domain produced similar modifications in the chromatin but resulted in an ,150-fold elevation in transcripts, approaching the level of transcription of an endogenous housekeeping gene. This rapidly inactivated kinetochores, causing a loss of assembled CENP-A and blocking further CENP-A assembly. Our data reveal that functional centromeres in vivo show a remarkable plasticity -kinetochores tolerate profound changes to their chromatin environment, but appear to be critically sensitive to the level of centromeric transcription.

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Section: Discussionmentioning

confidence: 58%

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

Bergmann

Jakubsche

Martins

et al. 2012

Journal of Cell Science

102

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“…The distribution of CENH3-containing nucleosomes within the boundaries of centromeres is not well understood, although it appears to be discontinuous and interspersed with canonical nucleosomes (Blower et al 2002;Yan et al 2008). Some human neocentromeres and several plant centromeres contain genes embedded as islands within centromeres (Saffery et al 2003;Nagaki et al 2004;Gong et al 2012). While genes may closely border CENH3-containing nucleosomes, gene transcription is generally incompatible with CENH3 (Ketel et al 2009).…”

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confidence: 99%

Maize centromeres expand and adopt a uniform size in the genetic background of oat

Wang

Zhang

et al. 2013

Genome Res.

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Most existing centromeres may have originated as neocentromeres that activated de novo from noncentromeric regions. However, the evolutionary path from a neocentromere to a mature centromere has been elusive. Here we analyzed the centromeres of nine chromosomes that were transferred from maize into oat as the result of an inter-species cross. Centromere size and location were assayed by chromatin immunoprecipitation for the histone variant CENH3, which is a defining feature of functional centromeres. Two isolates of maize chromosome 3 proved to contain neocentromeres in the sense that they had moved from the original site, whereas the remaining seven centromeres (1, 2, 5, 6, 8, 9, and 10) were retained in the same area in both species. In all cases, the CENH3-binding domains were dramatically expanded to encompass a larger area in the oat background (∼3.6 Mb) than the average centromere size in maize (∼1.8 Mb). The expansion of maize centromeres appeared to be restricted by the transcription of genes located in regions flanking the original centromeres. These results provide evidence that (1) centromere size is regulated; (2) centromere sizes tend to be uniform within a species regardless of chromosome size or origin of the centromere; and (3) neocentromeres emerge and expand preferentially in gene-poor regions. Our results suggest that centromere size expansion may be a key factor in the survival of neocentric chromosomes in natural populations.

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“…Figure 4 ChIP analysis of custom-made antibodies compared to purchased antibodies. The three diagrams (A-C) display the relative enrichment (Y-axis) of corresponding histone modifications at specific sites, as indicated by the primer numbers described previously [19]. All selected primers sites correspond to the regions in the rice chromosome 8 centromere.…”

Section: Assessment Of Antibody Suitability For Immunoprecipitation Amentioning

confidence: 99%

“…We selected six primer pairs corresponding to the sequences near the centromere of rice chromosome 8 reported previously [19] for the ChIP assay. As shown in Figure 4, all three of our site-specific antibodies essentially displayed the same histone modification patterns as the antibodies purchased from the Upstate Company.…”

Section: Assessment Of Antibody Suitability For Immunoprecipitation Amentioning

confidence: 99%

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels

et al. 2006

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In addition to DNA sequence information, site-specific histone modifications are another important determinant of gene expression in a eukaryotic organism. We selected four modification sites in common histones that are known to significantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of those site-specific modifications. We used these antibodies to demonstrate that the site-specific histone modification levels remain relatively constant in different organs of the same organism. We also compared the levels of selected histone modifications among several representative organisms and found that site-specific modifications are highly variable among different organisms, providing new insight into the evolutionary divergence of specific histone modifications.

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Sequencing of a rice centromere uncovers active genes

Cited by 487 publications

References 49 publications

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

Maize centromeres expand and adopt a uniform size in the genetic background of oat

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels

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