Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation

Liu, Hongjun; Ma, Langlang; Yang, Xuerong; Zhang, Lin; Zeng, Xing; Xie, Shupeng; Peng, Huanwei; Lin, Hung-Ching; Pan, Guangtang; Wu, Yongrui; Shen, Yaou

doi:10.1186/s12870-017-1055-x

Cited by 18 publications

(13 citation statements)

References 47 publications

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“…Our comparison between the callus and the seedling uncovered globally elevated methylation in the callus in all three sequence contexts. Consistently, hypermethylation in the callus relative to the immature embryo was found in a study that used another maize inbred line and methylated DNA immunoprecipitation sequencing (MeDIP-seq) data 48 . In this study, 24 nt small RNA was shown to be positively correlated with DNA methylation.…”

Section: Discussionsupporting

confidence: 62%

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Lin

Zheng

et al. 2020

Preprint

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The highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps. Genome comparison of A188 with the reference line B73 identified pervasive structural variation, including a 1.8 Mb duplication on the Gametophyte factor1 locus for unilateral cross-incompatibility and six inversions of 0.7 Mb or greater. Increased copy number of the gene, carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression together with low expression of yellow endosperm 1 (y1) condition reduced carotenoid accumulation, which accounts for the white seed phenotype of A188 that contrasts with the yellow seed of B73 that has high expression of y1 and low expression of the single-copy ccd1. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced expression of defense pathways and altered DNA methylation patterns of embryonic callus.

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Section: Discussionsupporting

confidence: 62%

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Lin

Zheng

et al. 2020

Preprint

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“…The mapping rate in our study was similar to that in P . trichocarpa leaves (41.41%) [ 27 ], but much lower than that in rice (~85%), maize (~93%) and cotton (~95%) [ 24 , 28 , 29 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of day/night DNA methylation differences in Populus nigra

Ding

Liang

et al. 2018

PLoS ONE

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DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra ‘N46’ at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.

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“…High levels of DNA methylation increase induction in Coffea canephora [45] and embryogenic cell formation in Arabidopsis T87 [46]. The MeDIP-seq profiles of maize [19,47] and WGBS profiles of regenerated rice [40] show a similar decrease in methylation upon regeneration. The modulation in DNA methylation may signify its role in re-differentiation, where hormone ratios determine organ identity in regeneration [48].…”

Section: Modulation Of Dna Methylation In Culture Is Crucial To Regenmentioning

confidence: 88%

“…In sugarcane, disease-resistant somaclones are induced by demethylating agents, such as 5-azaC [29]. Similarly, somaclonal variations in maize [19,47], Arabidopsis [74], rice [40] and several plant species may result from changes in DNA methylation. Altering DNA methylation can generate somaclones, which may offer some economic benefit; however, somaclonal variations are inconsistent and non-reproducible.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of the Methylome and Transcriptome during the Regeneration of Rice

et al. 2018

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Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture.

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Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation

Cited by 18 publications

References 47 publications

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Genome-wide analysis of day/night DNA methylation differences in Populus nigra

Dynamics of the Methylome and Transcriptome during the Regeneration of Rice

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