Understanding epigenomics based on the rice model

Lu, Yue; Zhou, Dao‐Xiu; Zhao, Yu

doi:10.1007/s00122-019-03518-7

Cited by 19 publications

(27 citation statements)

References 231 publications

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“…Error bars represent ± SD of three biological replicates (*P < 0.05, **P < 0.01, ***P < 0.001, two-tailed Student's t-test). (Lu et al, 2020). These histone modifications, in particular histone acetylation, function in the epigenetic regulation of gene expression and plant abiotic stress responses (Shen et al, 2015(Shen et al, , 2016Ueda and Seki, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Plant responses to environmental cues are usually linked to chromatin state (Chinnusamy and Zhu, 2009). There is accumulating evidence that histone modifications alter the structure of chromatin and play a vital role in the fine-tuning (Lu et al, 2020). These histone modifications, in particular histone acetylation, function in the epigenetic regulation of gene expression and plant abiotic stress responses (Shen et al, 2015(Shen et al, , 2016Ueda and Seki, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…The N-terminal tails of histone proteins contain chemical moieties that are targeted for modification by specific enzymes. Histone modifications, such as acetylation, methylation, and phosphorylation, regulate cellular processes by changing chromatin conformation (Lu et al, 2020). Alterations in chromatin structure either positively or negatively affect gene expression.…”

Section: Introductionmentioning

confidence: 99%

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Histone deacetylase HDA710 controls salt tolerance by regulating ABA signaling in rice

Ullah

Zhao

et al. 2021

JIPB

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Plants have evolved numerous mechanisms that assist them in withstanding environmental stresses. Histone deacetylases (HDACs) play crucial roles in plant stress responses; however, their regulatory mechanisms remain poorly understood. Here, we explored the function of HDA710/OsHDAC2, a member of the HDAC RPD3/HDA1 family, in stress tolerance in rice (Oryza sativa). We established that HDA710 localizes to both the nucleus and cytoplasm and is involved in regulating the acetylation of histone H3 and H4, specifically targeting H4K5 and H4K16 under normal conditions. HDA710 transcript accumulation levels were strongly induced by abiotic stresses including drought and salinity, as well as by the phytohormones jasmonic acid (JA) and abscisic acid (ABA). hda710 knockout mutant plants showed enhanced salinity tolerance and reduced ABA sensitivity, whereas transgenic plants overexpressing HDA710 displayed the opposite phenotypes. Moreover, ABA‐ and salt‐stress‐responsive genes, such as OsLEA3, OsABI5, OsbZIP72, and OsNHX1, were upregulated in hda710 compared with wild‐type plants. These expression differences corresponded with higher levels of histone H4 acetylation in gene promoter regions in hda710 compared with the wild type under ABA and salt‐stress treatment. Collectively, these results suggest that HDA710 is involved in regulating ABA‐ and salt‐stress‐responsive genes by altering H4 acetylation levels in their promoters.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Histone deacetylase HDA710 controls salt tolerance by regulating ABA signaling in rice

Ullah

Zhao

et al. 2021

JIPB

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“…However, deciphering the relationship between genetic and epigenetic variation remains a significant challenge ( Schulz et al., 2014 ; Alonso et al., 2016 ; Foust et al., 2016 ; Gugger et al., 2016 ; Herrera et al., 2017 ; Richards et al., 2017 ), and some studies have found that DNA methylation polymorphisms are explained by underlying genetic differences ( Becker et al., 2011 ; Li et al., 2014 ; Dubin et al., 2015 ), and therefore do not provide any additional sources of phenotypic variation. Although epigenetic variation among wild plant populations has been well studied, the changes in epigenetic variation involved in cultivation of plants remain poorly understood ( Piperno, 2017 ; Lu et al., 2020 ). In addition to studies comparing domesticated species to their wild progenitors ( Li et al., 2012 ; Sauvage et al., 2017 ), studies of crop plants with both natural and cultivated populations will shed light on the importance of epigenetic and genetic variation in domestication.…”

Section: Introductionmentioning

confidence: 99%

Comparisons of Natural and Cultivated Populations of Corydalis yanhusuo Indicate Divergent Patterns of Genetic and Epigenetic Variation

et al. 2020

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Epigenetic variation may contribute to traits that are important in domestication, but how patterns of genetic and epigenetic variation differ between cultivated and wild plants remains poorly understood. In particular, we know little about how selection may shape epigenetic variation in natural and cultivated populations. In this study, we investigated 11 natural populations and 6 major cultivated populations using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MS-AFLP or MSAP) markers to identify patterns of genetic and epigenetic diversity among Corydalis yanhusuo populations. We further explored correlations among genetic, epigenetic, alkaloidal, and climatic factors in natural and cultivated C. yanhusuo . We found support for a single origin for all cultivated populations, from a natural population which was differentiated from the other natural populations. The magnitude of F ST based on AFLP was significantly correlated with that for MSAP in pairwise comparisons in both natural and cultivated populations, suggesting a relationship between genetic and epigenetic variation in C. yanhusuo . This relationship was further supported by dbRDA (distance-based redundancy analyses) where some of the epigenetic variation could be explained by genetic variation in natural and cultivated populations. Genetic variation was slightly higher in natural than cultivated populations, and exceeded epigenetic variation in both types of populations. However, epigenetic differentiation exceeded that of genetic differentiation among cultivated populations, while the reverse was observed among natural populations. The differences between wild and cultivated plants may be partly due to processes inherent to cultivation and in particular the differences in mode of reproduction. The importance of epigenetic compared to genetic modifications is thought to vary depending on reproductive strategies, and C. yanhusuo usually reproduces sexually in natural environments, while the cultivated C. yanhusuo are propagated clonally. In addition, alkaloid content of C. yanhusuo varied across cultivated populations, and alkaloid content was significantly correlated to climatic variation, but also to genetic (6.89%) and even more so to epigenetic (14.09%) variation in cultivated populations. Our study demonstrates that epigenetic variation could be important in cultivation of C. yanhusuo and serve as a source of variation for response to environmental conditions.

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“…There has been rapid progress in the studies of the epigenome in rice, which has greatly advanced our understanding of epigenetics in plants and the findings are comparable in many ways to the dicot model Arabidopsis. In the paper entitled Understanding epigenomics based on the rice model, Lu et al (2020) provided a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, non-coding RNAs, and threedimensional genomics. They also discussed the challenges and perspectives along this line for future research in rice.…”

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confidence: 99%