Characterization of Eu- and Heterochromatin of <i>Citrus</i> with a Focus on the Condensation Behavior of 45S rDNA Chromatin

Abstract

To characterize the properties of eu- and heterochromatic regions in Citrus species, the chromosomal distribution of different histone H3 marks, DNA methylation sites (5mC) and 45S ribosomal DNA sites were determined for C. clementina, C. paradisi, C. sinensis, and for the hybrid Ortanique C. reticulata × C. sinensis. Our data show that in the relatively small genomes of investigated Citrus species (genome size ranges from 378–400 Mbp) the euchromatin is characterized by histone H3 lysine 4 mono-, di- and trimethylation (H3K4me1/ 2/3) and histone H3 lysine 9 trimethylation (H3K9me3). In contrast, histone H3 lysine 9 mono- and dimethylation (H3K9me1/2), histone H3 lysine 27 mono-, di- and trimethylation (H3K27me1/2/3) as well as 5-methylcytosine (5mC) were enriched at certain heterochromatin fractions. Whereas H3K9me1/2 and H3K27me1 were preferentially enriched at the chromomycin A₃-bright (CMA⁺) heterochromatin, H3K27me2/3 showed a higher accumulation at the DAPI brightly-stained heterochromatin. 5mC signals were associated with most of the CMA⁺ areas as well as with the DAPI strongly-stained heterochromatin fraction. Therefore, extensive methylation of DNA as well as of H3K9me1/2 and H3K27me1/2/3, and depletion of H3K4me1/2/3 and H3K9me3 appear to be specific features of heterochromatin in Citrus. Transcriptionally active decondensed 45S rDNA sites were found DNA hypomethylated, while the silenced condensed sites were strongly 5mC methylated. Although the number of chromosomal 45S rDNA sites differed between the species, the number of transcriptionally active rDNA sites remains constant.

Linked 5S and 45S rDNA Sites Are Highly Conserved through the Subfamily Aurantioideae (Rutaceae)

“…Furthermore, Yamamoto et al [2009] reported a single pair of 5S rDNA sites in chromosomes of Citropsis gabunensis, Citrus reshni, Fortunella japonica, Clymenia polyandra and Swinglea glutinosa and in 3 pairs in Poncirus trifoliata , but they did not investigate the position of 45S rDNA. Likewise, the number of 45S rDNA sites was previously reported for several Citrus species [Kang et al, 2008;Marques et al, 2011] and some related genera [Barros e Silva et al, 2010]. However, simultaneous detection of 5S and 45S rDNA sites in the same cell was previously reported only for P. trifoliata and Citrus species of the subgenus Citrus [Pedrosa et al, 2000;Carvalho et al, 2005;Brasileiro-Vidal et al, 2007;Moraes et al, 2007a, b].…”

Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

“…The largest 45S rDNA site in Z. biebersteiniana , for example, was hypermethylated, while the smallest was hypomethylated [Cremonini et al, 2003]. In another example, the levels of methylation in 45S rDNA sites were directly related to the condensation states observed in different species of the genus Citrus , and uncondensed and hypomethylated sites were found to be related to active genes [Marques et al, 2011]. Different lineages of A. suecica , however, demonstrated large variation in methylated 45S rDNA sites [Pikaard, 2002].…”

The Cytogenetic Map of the Poncirus trifoliata (L.) Raf.—A Nomenclature System for Chromosomes of All Citric Species

“…It is well-known that CMA + bands carrying 45S rDNA sites can be less bright or even neutral (Moraes et al 2007b) and may change the apparent size of the CMA + band at the microscopic level. Possibly, the epigenetic mechanisms involved in the regulation of the 45S rDNA expression (Pikaard 2000;Marques et al 2011) may influence the affinity of the CMA for its sequence.…”