Cytosine Methylation of an Ancient Satellite Family in the Wild Beet <b><i>Beta procumbens</i></b>

Abstract

DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

“…Therefore, to avoid a strong bias leading to false conclusions and interpretations with respect to the lower representation of satellite DNA sequences than that of other repeats in the reference sequence, we did not determine the methylation pattern of satellite DNA. Nevertheless, previously, we have extensively examined satellite cytosine methylation in sugar beet (Zakrzewski et al, 2011Schmidt et al, 2014) and observed high CHH methylation. The reason for the overall higher CHH methylation of sugar beet than that of Arabidopsis might be the elevated levels of CHH methylation in SINEs (Schwichtenberg et al, 2016) and in DNA transposons (this study) and the high abundance of retrotransposons with slightly higher CHH levels.…”

“…As genome-wide bisulfite sequencing is based on the reference sequence, bias will occur when the methylation pattern of satellite DNA is analyzed. Therefore, satellite DNA methylation has already been intensively investigated independently of the reference sequence by the sequencing of more than a thousand cloned bisulfite converted satellite mono-and multimers (Zakrzewski et al, 2011Schmidt et al, 2014).…”

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

“…Nonetheless, when additional sequence and annotation information of the genomic features become available, these data can be processed in the presented plant-RRBS data analysis pipeline for this research field. Currently, detailed cytosine methylation of repeats can be analyzed by cloned bisulfite-converted PCR products of repeat elements [43]. …”

Genome invasion by a hypomethylated satellite repeat in Australian crucifer Ballantinia antipoda

“…Based on the intensity of immunostaining signals, HSs appeared to be only poorly DNA methylated when compared with euchromatic chromosome arms and pericentromeric regions. A similar phenotype was described, based on cytogenetic studies, for centromeric repeats of A. thaliana , Beta vulgaris , Zea mays and Oryza sativa (Zhang et al ., ; Yan et al ., ; Zakrzewski et al ., , ); however, molecular analysis by bisulfite sequencing revealed that these repeats carried a good proportion of methylated cytosines (Zakrzewski et al ., , ; Schmidt et al ., ). In contrast, we found by both immunostaining and bisulfite sequencing that BaSAT1 repeats are hypomethylated.…”