**6. Micro RNA and epigenetic**

As well documented, about 80 % of human transcribed RNA is not translated into protein. This RNA was thought to be either functionless (Mattick, 2001), or transcriptional noise (Dennis, 2002). From this population, micro RNAs (miRNA) have an established epigenetic role with the potential to be implicated in programming. micro RNA (miRNA) are small untranslated RNAs generally 21-25 mucleotides in length (Bartel, 2004), they regulate gene expression by affecting the stability or the translation efficiency of target mRNA. They bind their complementary mRNA and thus dsRNA is formed, this recognized as foreign RNA and cleaved to be degraded. Matching between the miRNAs and mRNA doesn't have to be perfect as even incomplete binding can block translation (Mattick & Makunin, 2005). Nearly 30% of genes expression is probably regulated by miRNA via the interaction between miRNAs and their target mRNA. Individual miRNA may regulate 200 targets by partial base pairing to mRNA, sugessting that one miRNA may control numerous biological or pathological signaling pathway by affecting the expressions and functions of their targets. It has been reported that miRNA has a role in the development process (He & Hannon, 2004), including a role in the process of stem cell differentiation (Houbaviy et al., 2003). Also it has been shown in cancer studies of miRNA that DNA methylation and histone modification control the expression of these small RNAs. This was achieved by studying the effect of DNA demethylating agents and hisdtone deacetylases inhibitors on the expression of miRNA expression particularly the miR-127 which is embedded in CpG island (Saito & Jones, 2006;Saito et al., 2006).

### **7. Genomic imprinting**

Genomic imprinting is a developmental phenomenon that describes a unique form of gene regulation that leads to only one parental allele being expressed depending on its parental origin (Delaval & Feil, 2004;Surani, 1991). Insulin-like growth factor 2 (IGF2) and its receptor IGF2R are two of the first reported genes subjected to imprinting regulation (Barlow et al., 1991;DeChiara et al., 1991). In mouse genome there are 600 predicted imprinted genes (Luedi et al., 2005). These identified imprinted genes have a major common feature in that they are associated with at least one regulatory DNA element, often referred to as imprinted control region (ICR). The ICR region is essential in regulating the parental origin-specific

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another repressive histone mark, H3K9me2 (me3), this lysine methylation is catalyzed by several histone lysine methyltransferases, including SUV39H, SETDB1, G9a and GLP among others (Schultz et al., 2002;Lehnertz et al., 2003;Tachibana et al., 2005). Although the defined role of H3K9 methylation in epigenetic gene silencing remains elusive, one possible mechanism is that this mark can serve as a binding site for heterochromatin protein HP1, which has an intrinsic ability to recruit DNA methyltransferases to the silenced genes (Fuks

To establish DNA methylation in a subset of genes, polycomb protein EZH2 must associate with DNMTs (Esteller, 2007). It is thought that polycomb proteins could collaborate with DNMTs by recruiting them to silenced promoters to establish long-term silencing (Matarazzo et al., 2007). Leu et al (2004) investigated whether the removal of ERα signaling could cause changes in DNA methylation and chromatin structure of ERα target promoters. They used RNAi to transiently disable ERα in breast cancer cells and found that polycomb repressors and histone deacetylases assemble in the promoter of an ERα target gene. Accumulation of DNA methylation in these silenced targets like the PR promoter region then occurs and can be stably transmitted to cell progeny for long-term silencing. Both ERα expression and DNA demethylation appear to be required to restore PR expression. They also observed a trend that more ERα negative tumors had more methylated loci than ERα positive tumors (Leu et al., 2004). This indicates that dysregulation of normal signaling in cancer cells may result in stable silencing of downstream targets maintained by epigenetic

The epigenetic mechanisms for gene silencing involve the interplay between DNA methylation, histone modifications and nucleosomal remodeling. The families of methyl-CpG binding proteins (MBD and Kaiso families) have been identified to play a key role in this interplay. The molecular functions of methyl-CpG binding proteins are dependent on their ability to recognize and bind methylated DNA (Clouaire & Stancheva, 2008;Meehan et al., 1989; ing et al., 2006). Accumulating evidence suggests that methyl-CpG binding proteins can associate directly or indirectly with DNMTs, HDACs and HMTs and cooperate with them to modify chromatin structure and suppress initiation of gene transcription (Fuks et al., 2003;Jones et al., 1998;Kimura & Shiota, 2003;Sarraf & Stancheva, 2004). The associated partners of methyl-CpG binding proteins have also been found to include many nucleosomal remodeling complexes such as NuRD, CoREST, NCoR/SMRT, Sin3A, SUV39H and SWI/SNF (Fujita et al., 2003;Harikrishnan et al., 2005;Le Guezennec et al., 2006;Yoon et al., 2003;Wade et al., 1999;Zhang et al., 1999). The significant role of methyl-CpG binding proteins in cancer epigenetics is supported by the findings that they are localized to DNA hypermethylated and aberrantly silenced cancer genes (Bakker et al., 2002; Lopez-Serra et

Thus, it has been postulated that methyl-CpG binding proteins initially recognize and bind to methylated DNA, and then bring down nucleosomal remodeling complexes to modify chromatin to the repressive compact heterochromatin structure, which causes gene silencing. Inversely, the results from some other studies show that chromatin remodeling activities can further facilitate binding of methyl-CpG binding proteins to methylated DNA sites (Feng & Zhang, 2001;Harikrishnan, et al., 2005), suggesting interaction between methyl-CpG binding proteins and nucleosomal remodeling complexes results in mutual stimulation of each others' activity. Taken together, methyl-CpG binding proteins represent an important class of chromosomal proteins that associate with multiple protein partners to modify surrounding chromatin and silence transcription, providing a functional link between DNA methylation

and chromatin modification and remodeling (Lo & Sukumar, 2008).

et al., 2003;Lachner et al., 2001).

machinery (Dworkin et al., 2009).

al., 2006; Nguyen et al., 2001).

expression via interaction with specific transcription factors (Kim et al., 2007;Yang et al., 2003). Differential DNA methylation of the parental ICRs is one of the most common features associated with imprinted genes (Kim et al., 2003;Liang et al., 2000;Mancini-Dinardo et al., 2003). Typical disorders associated with imprinted genes include Prader-Willi and Angelman syndromes, Beckwith-Wiedemann syndrome and multiple forms of neoplasia (Weksberg et al., 2003;Zeschnigk et al., 1997). In addition to that, X inactivation is a mechanism that functionally equalizes the difference of X-linked genes between XX females and XY males by silencing one of the two X chromosomes in females. Dosage compensation is a widely known method of silencing the X chromosome in females. This is achieved epigenetically through a cascade of CpG methylation superimposed by global histone deacetylation (Avner & Heard, 2001;Lyon, 1999;Monk, 2002;Pfeifer et al., 1990).
