The Dominant and Poorly Penetrant Phenotypes of Maize <i>Unstable factor for orange1</i> Are Caused by DNA Methylation Changes at a Linked Transposon

Wittmeyer, Kameron T; Cui, Jin; Chatterjee, Debamalya; Lee, Tzuu‐fen; Tan, Qixian; Xue, Weiya; Jiao, Yinping; Wang, Po-Hao; Gaffoor, Iffa; Ware, Doreen; Meyers, Blake C.; Chopra, Surinder

doi:10.1105/tpc.18.00546

Cited by 25 publications

(12 citation statements)

References 80 publications

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“…Nevertheless, in recent years, the interest in reviving ancient colored sweet corn varieties or developing new pigmented varieties characterized by high content of carotenoids [311] and especially anthocyanins is increasing [305,[312][313][314][315][316] due to the potential functional properties of anthocyanin-rich genotypes [317,318], as well as to the increasing demand of natural colorants [22,319,320]. The biosynthesis of anthocyanins in maize aleurone (external part of the endosperm) and pericarp (external part of the kernel) of the kernels or in plant tissues involve over twenty structural and regulatory genes that have been identified and functionally characterized as reviewed by Petroni et al [305,[321][322][323]. The wide range of colors observed in maize kernels is mainly due to the biosynthesis and accumulation of carotenoids and flavonoids.…”

Section: Sweet Cornmentioning

confidence: 99%

Grown to Be Blue—Antioxidant Properties and Health Effects of Colored Vegetables. Part II: Leafy, Fruit, and Other Vegetables

et al. 2020

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The current trend for substituting synthetic compounds with natural ones in the design and production of functional and healthy foods has increased the research interest about natural colorants. Although coloring agents from plant origin are already used in the food and beverage industry, the market and consumer demands for novel and diverse food products are increasing and new plant sources are explored. Fresh vegetables are considered a good source of such compounds, especially when considering the great color diversity that exists among the various species or even the cultivars within the same species. In the present review we aim to present the most common species of colored vegetables, focusing on leafy and fruit vegetables, as well as on vegetables where other plant parts are commercially used, with special attention to blue color. The compounds that are responsible for the uncommon colors will be also presented and their beneficial health effects and antioxidant properties will be unraveled.

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Section: Sweet Cornmentioning

confidence: 99%

Grown to Be Blue—Antioxidant Properties and Health Effects of Colored Vegetables. Part II: Leafy, Fruit, and Other Vegetables

et al. 2020

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“…Another variant allele (E3M) which specified orange pericarp phenotype was analyzed and found to have some DNA methylation changes in the terminal sequences of the CI Ac and fAc elements. It is not clear whether these methylation differences are responsible for the differences in p2 expression; however, a previous study showed that TE DNA methylation can impact the expression of nearby genes (Wittmeyer et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition

Peterson

Zuo

2020

Preprint

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Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status and generating small RNAs. In this study, we demonstrated that Ac/fAc transposable elements are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of Class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events which involve the termini of two different, nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations and Composite Insertions (CIs). We identified over 50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is effected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate Composite Insertions that can control gene expression.

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“…In maize, the insertion of a CACTA-like TE into the promoter region of the photoperiod sensitivity modulator ZmCCT attenuates photoperiod sensitivity and accelerates postdomestication [ 41 ]. In addition, the expression of GRMZM2G053177 , a candidate maize gene that may participate in the regulation of flavonoid pigment production (e.g., phlobaphenes), is controlled by the DNA methylation status of the inserted CACTA TE [ 42 ]. Our results showed that 18 successive cytosines in the region downstream of the CACTA TE ( LOC_Os07g09540 ) were consistently demethylated by HNTs in the heat-tolerant rice strain (Fig.…”

Section: Discussionmentioning

confidence: 99%

Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance

Zhang

Zhang³

et al. 2020

BMC Genomics

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Background: High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence. Results: After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358-359 bp and 2-60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (ABA)-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_ Os01g19694). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains. Conclusions: After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.

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The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon

Cited by 25 publications

References 80 publications

Grown to Be Blue—Antioxidant Properties and Health Effects of Colored Vegetables. Part II: Leafy, Fruit, and Other Vegetables

Grown to Be Blue—Antioxidant Properties and Health Effects of Colored Vegetables. Part II: Leafy, Fruit, and Other Vegetables

Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition

Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance

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