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Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes

Wang, X.-l., Song, S.-h., Wu, Y.-s., Li, Y.-l., Chen, T.-t., Huang, Z.-y., Liu, S., Dunwell, T. L., Pfeifer, G. P., Dunwell, J., Wamaedeesa, R., Ullah, I., Wang, Y. and Hu, S.-n. (2015) Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. Journal of Experimental Botany, 66 (21). pp. 6651-6663. ISSN 0022-0957

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To link to this item DOI: 10.1093/jxb/erv372

Abstract/Summary

5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions,and mainly located in transposable element (TE) genes, especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.

Item Type:Article
Refereed:Yes
Divisions:Interdisciplinary centres and themes > Centre for Food Security
Faculty of Life Sciences > School of Agriculture, Policy and Development > Biodiversity, Crops and Agroecosystems Division > Crops Research Group
ID Code:41182
Publisher:Oxford University Press

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