| Epigenetics is the study of heritable traits that do not involve changes to their underlying DNA sequence. Epigenetic signals within the cell modulate particular transcriptional states (epigenetic states) necessary for the cell to “remember” previous stimulus events, including developmental signals and environmental changes (1). The molecular foundation of epigenetic signalling is the remodeling of chromatin, which occurs through a combination of (a) post-translational modification of amino acids in histone proteins, and (b) DNA methylation. The interplay between chromatin remodeling and other signaling molecules such as transcription factors and non-coding RNA controls the level and pattern of transcription from chromatin necessary to generate a given epigenetic state in the cell (2). The classic examples of epigenetic processes are cellular differentiation and maintenance of cell identity through multiple cell divisions over the lifetime of a multi-cellular organism (3).|
Epigenetic signals can be divided into two main categories, cis- and trans-. Trans-epigenetic states are primarily self-propagating transcriptional states maintained via feedback loops and transcription factor (TF) networks (4). For example, if an external stimulus causes a TF to activate its own transcription, the result is a (trans) epigenetic state that becomes self-sustaining when the stimulus is removed, and continues after cell division. Small RNAs (sRNAs) also sometimes function as trans-epigenetic signals (5). Trans-epigenetic states are often found in prokaryotes and single-celled eukaryotes, where they support cellular memory.
Fig 1 : Modification : 5-Me-dC
Fig 2 : Modification : 5-OH medC
Cis-epigenetic signals, by contrast, are actually physically associated, and inherited, with the particular chromosome upon which they act. Covalent modification of histones (the protein part of chromatin) and DNA methylation (typically by the conversion of deoxycytosine (dC) to 5-methyl-dC by various DNA methyltransferase enzymes) are key examples of cis-epigenetic signaling processes (6). For example, whenever two identical DNA sequences in the same cell are differentially regulated, they are under the control of a cis-epigenetic process. Genomic imprinting (the specific expression of either the maternal or paternal gene in a cell) and X-chromosome inactivation in mammals are both cis-epigenetic phenomenon (7).|
Of cis-epigenetic processes, DNA methylation in higher eukaryotes is the best known and studied. 5-methyl-dC is most commonly found in CpG sites near promoters (~ 75% of CpGs are methylated in somatic cells), being associated with gene silencing, or at least a significant reduction in transcriptional activity. The ability of DNA methylation to thus regulate the timing and pattern of DNA transcription is critical to the process of cell differentiation and proper embryonic development in mammals (8). As part of the process of embryonic development, both genomic imprinting and X-chromosome inactivation (which is necessary to properly dosage-compensate X-linked genes) is controlled by DNA methylation. DNA methylation also acts to suppress the expression and mobility of repetitive DNA such as LINE (long interspersed nuclear elements) in genomic DNA; indeed, de-methylation of LINEs can be a trigger for initiation of tumorigenesis. Recent work on the frequency of observed DNA methylation changes in cancer patients suggests that monitoring such changes may prove beneficial in diagnosis and treatment (9).
The establishment of cis-epigenetic states is mediated by TFs (10), sRNAs, and non-coding RNAs (ncRNAs) (11). Recent work has established that sRNAs affect epigenetic states in fission yeast (S. pombe) and Arabidopsis (5). Plants utilize sRNAs to repress transposons and regulate gene expression via RNA-dependent DNA methylation (12). Both small and long ncRNA have been proposed as establishment signals for cis-epigenetic states, primarily as “bridges” between chromatin modifiers (usually proteins) and genomic DNA (13, 14). These ncRNA molecules might act globally by directing chromatin modifiers to specific target loci (15), or more locally to establish cis-epigenetic states in the same genomic region from which they are transcribed (14).
While the importance of 5-methyl-dC in epigenetics is well-known, recent research work suggests that a second methylated nucleotide, 5-hydroxymethyl-dC (5-hm-dC), may also play a role. In 2009, Kriaucionis and Heintz reported the presence of high levels of 5-hm-dC in Purkinje neurons from mouse brain tissue, with the 5-hm-dC specifically localized to CpG regions (16). Although the presence of 5-hm-dC in mouse and rat brain tissue was first reported in the 1970’s (17,18), this new report significantly expands on this by definitively localizing 5-hm-dC to CpG regions of DNA, thereby suggesting that this modified base may play an important epigenetic regulatory role in the central nervous system of mammals. Shortly thereafter, Tahiliani et al. reported that the enzyme TET1 catalyzed the conversion of 5-methyl-dC to 5-hm-dC, both in vitro and in vivo, strengthening the case for such a role (19). Elucidating the possible epigenetic function of 5-hm-dC in the cell is currently a very active area of research.
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