Dicer-independent RNA-directed DNA methylation in Arabidopsis

Yang, Donglei; Zhang, Guiping; Tang, Kai; Li, Jingwen; Yang, Lan; Huang, Huan; Zhang, Heng; Zhu, Jian‐Kang

doi:10.1038/cr.2015.145

Cited by 104 publications

(115 citation statements)

References 67 publications

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“…The overall results showed that the fruit could be a potential source of sugar, flavonoid and total fat. The results are in good agreement with the reported literature [33,34].…”

Section: Resultssupporting

confidence: 83%

Chemical Composition of Three Nitraria Species Fruits

Yuan¹,

Sun²,

Yi³

et al. 2018

Asian J. Chem.

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In this study, the chemical compositions of fruits Nitraria roborowskii Kom., Nitraria sibirica Pall., Nitraria tangutorum Bobr. were investigated. The highest total flavonoids content were observed in Nitraria sibirica, which had the highest crude protein content (6.60 %), followed by Nitraria tangutorum (3.07%) and Nitraria roborowskii (2.65 %). The total sugar content of Nitraria species varied between 4.66 % and 5.31 %, total fat between 0.143 and 0.537 %, pH 3.81 and 4.29, respectively. Mineral compositions of the Nitraria species were 4530.2 mg/g Na, 3778.9 mg/g K, 681.0 mg/g Ca, 349.0 mg/g Mg, 301.8 mg/g P, 25.2 mg/g Fe, 4.3mg/g B, 2.6 mg/g Sr, 1.1 mg/g Co and 0.6 mg/g Cr.

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“…The overall results showed that the fruit could be a potential source of sugar, flavonoid and total fat. The results are in good agreement with the reported literature [33,34].…”

Section: Resultssupporting

confidence: 83%

Chemical Composition of Three Nitraria Species Fruits

Yuan¹,

Sun²,

Yi³

et al. 2018

Asian J. Chem.

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“…3) were evaluated for significance using a block-bootstrap method. 58 The Class F loci showed significant overlap with all histone modifications, with particularly large numbers of overlaps being observed with H3K27me1 and K3K9me2, in line with observations made by Yang & Zhang et al, 59 who also identified overlap between these histone marks and DCL-independent methylation. The apparent constitutive heterochromatin at the F loci may account for the dependence of CHG F type loci on DDM1.…”

Section: Classes Of Interaction and Histone Modificationsupporting

confidence: 72%

“…We found that most classes of sRNA loci are enriched for overlap with H3K9me2 and H3K27me1, recently identified as enriched within subclasses of RdDM loci. 59 The C24-specific sRNAs do not show this enrichment, likely due to differences between loci of histone modifications between ecotypes.…”

Section: Classes Of Interaction and Histone Modificationmentioning

confidence: 99%

Mobile small RNAs and their role in regulating cytosine methylation of DNA

Hardcastle

Lewsey

2016

RNA Biology

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Small (s)RNAs of 21 to 24 nucleotides are associated with RNA silencing and methylation of DNA cytosine residues. All sizes can move from cell-to-cell and long distance in plants, directing RNA silencing in destination cells. Twenty-four nucleotide sRNAs are the predominant long-distance mobile species. Thousands move from shoot to root, where they target methylation of transposable elements both directly and indirectly. We derive several classes of interaction between small RNAs and methylation and use these to explore the mechanisms of methylation and gene expression that associate with mobile sRNA signaling.

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“…The relative histone modification abundance was defined as n(Histone) 3 N(Input)/(N(Histone) 3 n(Input)), where n() is the sum of the reads in the TSS-surrounding regions and N() is the number of all the mapped reads. Histone and Input represent the specific histone modification and ChIP input, respectively (Yang et al, 2016).…”

Section: Defining the Ortholog Relationshipmentioning

confidence: 99%

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes

et al. 2016

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Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.Gene duplication, which generates extra copies from ancestral genes, can provide raw materials for developing new functions and is one major means of contributing to the evolution of genomic novelty

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Dicer-independent RNA-directed DNA methylation in Arabidopsis

Cited by 104 publications

References 67 publications

Chemical Composition of Three Nitraria Species Fruits

Chemical Composition of Three Nitraria Species Fruits

Mobile small RNAs and their role in regulating cytosine methylation of DNA

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes

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