The centromere is a chromosomal region where the kinetochore is formed, which is the attachment point of spindle fibers. Thus, it is responsible for the correct chromosome segregation during cell division. Telomeres protect chromosome ends against enzymatic degradation and fusions, and localize chromosomes in the cell nucleus. For this reason, centromeres and telomeres are parts of each linear chromosome that are necessary for their proper functioning. More and more research results show that the identity and functions of these chromosomal regions are epigenetically determined. Telomeres and centromeres are both usually described as highly condensed heterochromatin regions. However, the epigenetic nature of centromeres and telomeres is unique, as epigenetic modifications characteristic of both eu- and heterochromatin have been found in these areas. This specificity allows for the proper functioning of both regions, thereby affecting chromosome homeostasis. This review focuses on demonstrating the role of epigenetic mechanisms in the functioning of centromeres and telomeres in plants and animals.

In most cereals, coding sequences account for less than 20% of the genome (Flavell et al., 1977;Barakat et al., 1997); the remaining part is composed mainly of repetitive sequences, among which microsatellites and retrotransposons are of particular importance. Retrotransposons are ubiquitous and abundant components of grass genomes, constituting a major fraction of repetitive sequences (approximately 10%-60% of the genome). In many species there is a positive correlation between the copy number of retrotransposons and genome size (Pearce et al., 1996;Vicient et al., 2001;Schulman et al., 2004). It is thought that even among individuals within one population there are differences in copy numbers of a given retrotransposon. Retrotransposons are excellent tools for detecting genetic diversity as they are major generators of genomic changes. Sequences generated from retrotransposon-based molecular markers are often more polymorphic than sequences generated from random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), or restriction fragment length polymorphism (RFLP). Detection of inter-retrotransposon amplified polymorphisms (IRAPs) became a retrotransposon-based fingerprinting technique. IRAP markers are generated by amplification of sequences, embedded between 2 retrotransposons, using outward-facing primers annealing to long terminal repeat (LTR) target sequences. This marker system was used for the first time in barley, based on the BARE-1 retrotransposon (Kalendar et al., 1999;Vicient et al., 1999). It was also used in genetic studies of the diversity or phylogenetic relationships of Oryza L.

Main conclusion The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations.This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes. Wheat chromosomes were eliminated to a higher extent. The lower content of telomeric heterochromatin was also found in rye chromosomes in comparison with parental rye. Studying the location of selected retrotransposons from Ty1-copia and Ty3-gypsy families using fluorescence in situ hybridization revealed additional locations of these retrotransposons that were not present in chromosomes of parental species. ISSR, IRAP and REMAP analyses showed significant changes at the level of specific DNA nucleotide sequences. In most cases, the disappearance of certain types of bands was observed, less frequently new types of bands appeared, not present in parental species. This demonstrates the scale of genome rearrangement and, above all, the elimination of wheat and rye sequences, largely due to the reduction of chromosome number. With regard to the proportion of wheat to rye genome, the rye genome was more affected by the changes, thus this study was focused more on the rye genome. Observations suggest that genome reorganization is not finished in the F5 generation but is still ongoing in the F8 generation.

Polyploidy is an important event and major force in plant speciation. Amongst the polyploids, allopolyploids have attracted special attention to investigate genetic and epigenetic mechanisms. Also, they are the means for the development of new genotypes and genomic combinations to facilitate genetic enhancement and agricultural productivity. Whereas natural allopolyploids are genetically stable and well adapted, the newly synthesized ones are highly unstable. This instability is manifested into alterations at genomic and/or phenotypic level. Here we present the phenomenon of direct chromosome/chromatin elimination from pollen mother cells (PMCs) in wheat-rye hybrids as one aspect of instability leading to irregular meiosis and disturbances in meiotic process. One of the prominent irregularities noticed is peripherally separated uncondensed or pycnotic masses of chromatin in all meiotic stages. We have observed that this chromatin undergoes elimination by budding-like way, whereby a "mini-cell" is created. It was also found that nucleoli are the first to be eliminated along with a small mass of chromatin. By means of GISH we have shown that both rye and wheat chromatin might be eliminated. In the separated groups of chromosomes/ chromatin neither DNaseI nor DNase II activity was detected. Immunolocalization of tubulin allowed for differentiation between chromatin elimination from microspores and elimination from earlier stages of meiosis. It was noticeable, that in microspores special cytoskeleton structure pushing micronuclei out from the cells was created. Elimination occurred before and after meiosis as well as in each stage of meiotic division, but its intensity varied, depending on the PMC. The basis of the elimination mechanism might be the same as in cytomixis, because both phenomena share common symptoms, although cytomixis per se was rare in the analyzed hybrids.

Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.