The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes

Abstract

The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

“…The immunolocalization approach, a visual and qualitative technique, can be applied to all plant species. It has been used to detect DNA methylation patterns in Arabidopsis (Fransz et al, 2002;Tessadori et al, 2007), 5mC distribution patterns in Secale cereale and Capsella bursa-pastoris (Kalinka and Achrem, 2020;Gomez-Cabellos et al, 2022), and changes in histone methylation during microspore reprogramming to embryogenesis in rapeseed and barley (El-Tantawy et al, 2014;Rodrıǵuez-Sanz et al, 2014a), and during stress-induced pollen reprogramming in rapeseed (Solıś et al, 2012). Santamarıá et al (2009) analyzed genomic DNA methylation patterns during bud set and bud burst in Castanea sativa and Pérez et al (2015) during different embryo developmental stages in cork oak.…”

Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes

“…The study showed a high correlation between 5mC and 5hmC levels in different tissues of all the rye species, suggesting co-existence of the two modified bases. Furthermore, by comparing the chromosomal distribution of 5mC ( Kalinka and Achrem, 2020 ) and 5hmC, Kalinka et al (2023) were able to show that the two modified bases occur in the same regions of the chromosome. Importantly, both the modified bases were found to be absent in a large heterochromatin region, suggesting that 5hmC presence might be linked to coding rather than non-coding sequences in rye, in contrast to rice.…”