Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives

He, Shibin; Yan, Shihan; Wang, Pu; Zhu, Wei; Wang, Xiangwu; Shen, Yue; Shao, Kejia; Xin, H. P.; Li, Shaohua; Li, Lijia

doi:10.1371/journal.pone.0097364

Cited by 21 publications

(16 citation statements)

References 44 publications

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“…Although in prior work we did not find a clear H3K9me2 knob staining pattern in meiotic chromosome spreads or interphase mitotic root cells (Shi and Dawe, 2006), more recent cytogenetic data from root tip chromosomes (He et al, 2014) and ChIP-seq data from developing ear tissue reported herein clearly show that knobs are marked by H3K9me2 ( Figure 3C). Neither type of knob repeat showed any evidence of RdDM as assayed by 24-nucleotide siRNAs (Supplemental Figure 4A).…”

Section: Discussioncontrasting

confidence: 68%

“…At a molecular level, the most thorough descriptions of maize heterochromatin have been related to DNA methylation and siRNAs (Eichten et al, 2011;Gent et al, 2013;Regulski et al, 2013). Multiple other studies have provided valuable insights into the distribution of DNA methylation, nucleosomes, and histone modifications (Eichten et al, 2012;Fincher et al, 2013;Labonne et al, 2013;Makarevitch et al, 2013;He et al, 2014;Madzima et al, 2014). These studies have been limited in their application to heterochromatin, however, because of poor resolution over repetitive regions, shortage of experimental data, or a focus on genic chromatin.…”

Section: Introductionmentioning

confidence: 99%

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Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

et al. 2014

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RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.

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Section: Discussioncontrasting

confidence: 68%

Section: Introductionmentioning

confidence: 99%

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

et al. 2014

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“…The correlation between late terminal condensation region and H3K4me2 was also reported for Costus spiralis and Eleutherine bulbosa (Feitoza and Guerra 2011) as well as for inbred lines and hybrids of maize (Shi and Dawe 2006;He et al 2014). In Dimethylation in histone H3 lysine 9 is a characteristic heterochromatin mark (Feng and Jacobsen 2011), which is important for transposon silencing and for DNA methylation control (Bernatavichute et al 2008).…”

Section: Discussionsupporting

confidence: 59%

Chromosomal distribution of H3K4me2, H3K9me2 and 5-methylcytosine: variations associated with polyploidy and hybridization in Brachiaria (Poaceae)

2016

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Assessment of chromosomal distribution of modified histones and 5-methylcytosine shown that there are diversification of chromosomal types among species of Brachiaria and its interspecific hybrids. Histone post-translational modifications and DNA methylation are epigenetic processes that are involved in structural and functional organization of the genome. This study compared the chromosomal distribution of modified histones and 5-methylcytosine (5-mCyt) in species and interspecific hybrids of Brachiaria with different ploidy levels and reproduction modes. The relation between H3K9me2 and 5-mCyt was observed in the nucleolus organizer region, centromeric central domain and pericentromeric region. H3K4me2 was detected in euchromatic domains, mainly in the terminal chromosomal regions. Comparison of chromosomal distribution among species and hybrids showed greater variation of chromosomal types for the H3K9me2 in B. decumbens (tetraploid and apomictic species) and the 963 hybrid, while, for the H3K4me2, the variation was higher in B. brizantha and B. decumbens (tetraploid and apomictic species) and 963 hybrid. The chromosome distribution of 5-mCyt was similar between B. brizantha and B. decumbens, which differ from the distribution observed in B. ruziziensis (diploid and sexual species). Significant alterations in DNA methylation were observed in the artificially tetraploidized B. ruziziensis and in the interspecific hybrids, possibly as result of hybridization and polyploidization processes. The monitoring of histone modifications and DNA methylation allowed categorizing nuclear and chromosomal distribution of these epigenetic marks, thus contributing to the knowledge of composition and structure of the genome/epigenome of Brachiaria species and hybrids. These data can be useful for speciation and genome evolution studies in genus Brachiaria, and represent important markers to explore relationships between genomes.

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“…In wild-type Arabidopsis, CO suppression around the centromere closely reflects the increase in DNA methylation (23,38,55). In contrast, DNA methylation in maize (56) does not follow the same strongly U-shaped distribution pattern as COs (Fig. 1C).…”

Section: Mechanistic Underpinnings Of Dsb Hotspot Recognition In Maizementioning

confidence: 90%

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

Wang

Dukowic-Schulze

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

151

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Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.

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Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives

Cited by 21 publications

References 44 publications

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

Chromosomal distribution of H3K4me2, H3K9me2 and 5-methylcytosine: variations associated with polyploidy and hybridization in Brachiaria (Poaceae)

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

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