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

Abstract

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 elements (TEs), 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.

Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond

“…The findings suggest that 5-hmC may not be present in biologically relevant quantity in the plant genome (Erdmann et al, 2015). Studies on three rice cultivars indicated that 5-hmC is present at very low quantity (1.39 to 2.17 per million nucleosides) especially in TEs and heterochromatin regions (Wang et al, 2015). Moreover, the occurrence of 5-hmC was detected in the inactive TEs.…”

“…It is not yet clear that 5-hmC is implicated in what type of cellular processes in the animal system, and its epigenetic relevance is yet to be understood (Klungland and Robertson, 2017). Hence, existence and epigenetic role of 5-hmC, if any, is yet to be discovered in plants (Terragni et al, 2012; Moricová et al, 2013; Wang et al, 2015). These findings rejuvenate interest in understanding the epigenetics of 5-hmC, and hence 5-hmC is now considered as the sixth base of the epigenome (Shi et al, 2017).…”

Ascorbic Acid and Ozone: Novel Perspectives to Explain an Elusive Relationship

“…The presence of an appreciable level of hydroxymethylcytosine in plant cells has been questioned [86], but further studies detected it in significant amounts in rice cultivars [87]. Remarkably, early studies in mammal cells failed to detect hydroxymethylcytosine in several cell types, although it is now clear that the hydroxylation of methylcytosine is widespread in animals [85].…”

How to Design a Whole-Genome Bisulfite Sequencing Experiment

“…This has to be taken into account for organisms/cell types with substantial amounts of 5hmC, such as the cerebellum cells of Parkinson disease patients [13]. In plants, 5hmC is of minor relevance [14], as it occurs only in very low amounts and may merely serve as an intermediate product during demethylation [15].…”