Heterochromatin upholds several critical functions which are important for the cell. Heterochromatin can either be constitutive or facultative both of which plays a major role in expression of genes. Importance of heterochromatin reflects as to why plants use several pathways to maintain it. Here we will discuss some of these pathways.
Two states of chromatin are known as euchromatin and heterochromatin. Tightly packed form of DNA is called heterochromatin which is enriched at the centromeres and telomeres of chromosomes. The dense packing of DNA makes it less accessible to several protein factors and hence is often described as the gene-poor part of the genome. Heterochromatin is primarily composed of highly repetitive sequences such as satellite sequences, ribosomal DNA (rDNA) and transposable elements (1). It localizes at the nuclear periphery and nucleolus. Its formation involves recruitment of histone-binding factors. Propagation of heterochomatic status involves several epigenetic modifications such as DNA methylation, histone variants, non-coding RNA and histone modifications, methylation of histone H3 at lysine 9 being the distinct one.
Besides CpG methylation, plants also have non-CpG methylation throughout its development. DNA methylation occurs at three different contexts namely, CG, CHG and CHH, where H is either A, C or T. Different proteins play roles in different contexts. DNA methylation depends on METHYLTRASFERASE1 (MET1) for CG, CHROMOMETHYLASE3 (CMT3) for CHG and DOMAIN REARRANGED METHYLTRANSFERASE2 (DRM2) for CHH (2, 3, 4). Dimethylation of H3K9 (H3K9me2) is mainly associated with the heterochromatic transposable elements (TEs) (5). CHG-containing oligonucleotides are directly bound by the SRA domain of the H3K9 methyltransferase KRYPTONITE (KYP) (6). A self-reinforcing loop was suggested, in which methylated CHG DNA recruits KYP to maintain methylation of H3K9 whereas H3K9me2 recruits CMT3 to methylate CHG (3, 6). During several rounds of replication if methylation is not properly maintained then the fully methylated DNA can become hemimethylated and eventually unmethylated DNA. In order to prevent this CMT3 acts as a maintenance methyltransferase by efficiently converting hemimethylated DNA to fully methylated DNA. One plausible model suggested to imply that methylation of CMT3 takes place during DNA replication is that either CMT3 is displaced from nucleosome during replication and is recruited back to the methylated newly assembled nucleosomes after the completion of replication or CMT3 may be recruited to the chromatin by pre-modified H3K9me2 marks from parental histones during DNA replication (7). A dual-recognition mechanism ensures a higher fidelity of CHG DNA methylation, in which the CMT3 bromo adjacent homology (BAH) and chromo domains simultaneously read the H3K9me2 on the two tails emanating from a single nucleosome.
Histone codes, marks and variants
Core histones H2A,...