Disrupted Genome Methylation in Response to High Temperature Has Distinct Affects on Microspore Abortion and Anther Indehiscence

Ma, Yizan; Ling, Min; Wang, Maojun; Wang, Chaozhi; Zhao, Yunlong; Li, Yaoyao; Fang, Qidi; Wu, Yuanlong; Xie, Sai; Ding, Yuanhao; Su, Xiaojun; Hu, Qin; Zhang, Qinghua; Li, Xueyuan; Zhang, Xianlong

doi:10.1105/tpc.18.00074

Cited by 93 publications

(79 citation statements)

References 69 publications

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“…Furthermore, sequence regions enriched for CHH are already elaborately studied by others (see e.g. [13,14,29,41,43,44].…”

Section: In Plants Lmrs Are Abundant In Chg Context and Not In Cg Conmentioning

confidence: 99%

In plants distal regulatory sequences overlap with unmethylated rather than low-methylated regions, in contrast to mammals

Hoefsloot

Stam

2020

Preprint

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Background: DNA methylation is an important factor in the regulation of gene expression and genome stability. High DNA methylation levels are associated with transcriptional repression. In mammalian systems, unmethylated, low methylated and fully methylated regions (UMRs, LMRs, and FMRs, respectively) can be distinguished. UMRs are associated with proximal regulatory regions, while LMRs are associated with distal regulatory regions. Although DNA methylation is mainly limited to the CG context in mammals, while it occurs in CG, CHG and CHH contexts in plants, UMRs and LMRs were expected to occupy similar genomic sequences in both mammals and plants. Results:This study investigated major model and crop plants such as Arabidopsis thaliana, tomato (Solanum lycopersicum), rice (Oryza sativa) and maize (Zea mays), and shows that plant genomes can also be subdivided in UMRs, LMRs and FMRs, but that LMRs are mainly present in the CHG context rather than the CG context. Strikingly, the identified CHG LMRs were enriched in transposable elements rather than regulatory regions. Maize candidate regulatory regions overlapped with UMRs. LMRs were enriched for heterochromatic histone modifications and depleted for DNase accessibility and H3K9 acetylation. CHG LMRs form a distinct, abundant cluster of loci, indicating they have a different role than FMRs. Conclusions: Both mammalian and plant genomes can be segmented in three distinct classes of loci, UMRs, LMRs and FMRs, indicating similar underlying mechanisms. Unlike in mammals, distal regulatory sequences in plants appear to overlap with UMRs instead of LMRs. Our data indicate that LMRs in plants have a different function than those in mammals. Background Epigenetic marks, including DNA methylation and histone modifications, are important factors involved in regulating chromatin structure and gene expression. In both animals and plants, high levels of DNA methylation lead to less accessible chromatin and have been associated with transcriptional repression, while low DNA methylation has been observed at active distal and proximal gene regulatory regions and gene bodies [1-6].Overall, functions of DNA methylation, such as silencing of transposable elements, genome stability and 3 transcription regulation, are similar in plants and mammals [1,2,[6][7][8]. There are also functions that are identified for mammals, but not yet reported for plants, such as a widespread tissue-specific demethylation of regulatory elements and inhibition of cryptic initiation of transcription [6,[9][10][11]. One well-known difference between animals and plants is that while animals have primarily methylation in CG context in most tissues, plants also have abundant methylation in CHG, and low methylation levels in CHH context (where H is A, T or C) [1,12]. Although the DNA methylation pathways are quite conserved through the plant kingdom they also display differences [11][12][13]. As the vast majority of the mechanistic insight into DNA methylation is obtained in Arabidopsis, below the pathways are d...

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“…Furthermore, sequence regions enriched for CHH are already elaborately studied by others (see e.g. [13,14,29,41,43,44].…”

Section: In Plants Lmrs Are Abundant In Chg Context and Not In Cg Conmentioning

confidence: 99%

In plants distal regulatory sequences overlap with unmethylated rather than low-methylated regions, in contrast to mammals

Hoefsloot

Stam

2020

Preprint

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“…High rates of glucose metabolism may promote fatty acid synthesis in order to promote the anther development of cotton [59]. Researchers studying cotton (Gossypium hirsutum) anthers under a high temperature (HT) and normal temperature (NT) indicated that HT disturbs sugar and ROS metabolism by disrupting DNA methylation, leading to microspore sterility [60]. Flavonoids play an important role in the formation of pollen exine formation, pollen germination, and the fertility of several plants that are key branch-point genes during tetrad and uninucleate microspore periods.…”

Section: Transcriptome Mrna In the Anther Development Of Cottonmentioning

confidence: 99%

Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

Qin

Dong

et al. 2019

Genes

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Cotton plays an important role in the economy of many countries. Many studies have revealed that numerous genes and various metabolic pathways are involved in anther development. In this research, we studied the differently expressed mRNA and lncRNA during the anther development of cotton between the cytoplasmic male sterility (CMS) line, C2P5A, and the maintainer line, C2P5B, using RNA-seq analysis. We identified 17,897 known differentially expressed (DE) mRNAs, and 865 DE long noncoding RNAs (lncRNAs) that corresponded to 1172 cis-target genes at three stages of anther development using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DE mRNAs; and cis-target genes of DE lncRNAs probably involved in the degradation of tapetum cells, microspore development, pollen development, and in the differentiation, proliferation, and apoptosis of the anther cell wall in cotton. Of these DE genes, LTCONS_00105434, LTCONS_00004262, LTCONS_00126105, LTCONS_00085561, and LTCONS_00085561, correspond to cis-target genes Ghir_A09G011050.1, Ghir_A01G005150.1, Ghir_D05G003710.2, Ghir_A03G016640.1, and Ghir_A12G005100.1, respectively. They participate in oxidative phosphorylation, flavonoid biosynthesis, pentose and glucuronate interconversions, fatty acid biosynthesis, and MAPK signaling pathway in plants, respectively. In summary, the transcriptomic data indicated that DE lncRNAs and DE mRNAs were related to the anther development of cotton at the pollen mother cell stage, tetrad stage, and microspore stage, and abnormal expression could lead to anther abortion, resulting in male sterility of cotton.

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“…Several studies have demonstrated that DNA methylation causing epigenetic variation in crop plants has its role in tolerance to heat stress. For example, in cotton, high temperature disrupted the genome methylation leading to pollen abnormalities, and heat tolerant lines showed an overall high level of genome‐wide DNA methylation compared with sensitive lines (Ma et al, 2018). These DNA methylations have occurred in the genes involved in the starch, auxin, and sugar metabolic pathways that are crucial for proper pollen development (Min et al, 2014).…”

Section: Future Ways For Tackling the Problem Of Heat Stressmentioning

confidence: 99%

Breeding, genetics, and genomics for tolerance against terminal heat in lentil: Current status and future directions

2020

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Heat stress at terminal stage in lentil is one of the major factors causing drastic yield loss. Development of heat tolerant cultivars is one of the ways to tackle this problem. However, heat stress tolerance is a complex trait in nature and many morphological, physiological, biochemical, and metabolic changes are responsible for heat stress tolerance in lentil. Therefore, in the past years, efforts have been made to know genetics and genomics of heat stress tolerance in lentil. In this review, we discussed current progress on breeding, genetics, and genomics including quantitative trait locus (QTL) mapping, transcriptomics, proteomics, and network of metabolic pathways for heat tolerance and future directions for developing heat tolerant cultivars in lentil.

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Disrupted Genome Methylation in Response to High Temperature Has Distinct Affects on Microspore Abortion and Anther Indehiscence

Cited by 93 publications

References 69 publications

In plants distal regulatory sequences overlap with unmethylated rather than low-methylated regions, in contrast to mammals

In plants distal regulatory sequences overlap with unmethylated rather than low-methylated regions, in contrast to mammals

Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

Breeding, genetics, and genomics for tolerance against terminal heat in lentil: Current status and future directions

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