| CpG Islands |
Both PRC1 and PRC2 are known to co-localize with CpG islands [70]. CpG islands associate with promoter elements of active genes and remain methylation-free, in contrast to lone CpG dinucleotides which are highly subject to cytosine methylation (reviewed in [148]). The percentage of CpG sites in the HIV LTR does not meet the canonical definition of a CpG island, however studies of latent HIV in resting CD4+ T-cells suggests they are not subject to methylation [14,149,150] and furthermore that methylation of the LTR is highly repressive [151,152]. While the role for DNA methylation itself in latency is greatly debated [14,149-154], these elements may act as a marker for an intragenic promoter [155] and play a role in recruitment of PRC2. |
| ncRNAs |
Noncoding RNAs have been identified as major regulators of gene silencing during development. Two of the most studied ncRNA mechanisms, X-chromosome inactivation and HOX gene silencing by their cognate ncRNAs XIST and HOTAIR, have defined PRC2 binding and recruitment by these ncRNAs as critical for establishment of transcriptional repression (reviewed in [156]). PRC2 core proteins EZH2, SUZ12 and accessory protein JARID2 have all been demonstrated to have RNA binding domains critical to this recruitment mechanism [157,158]. Knockdown of an HIV-expressed antisense RNA has been shown to decrease EZH2 at the LTR and increase transcriptional activation, however they were unable to establish a definitive role in a primary CD4+T-cell model [159]. |
| H3K36 and the PCL Proteins |
Sub-stoichiometric components of the PRC2 complex, the PCL proteins recognize H3K36me3, a mark traditionally found within the gene bodies of transcriptionally active genes. The PCL proteins were shown to simultaneously recruit the H3K36 demethylase KDM2B (NO66), the H3K4 demethylase KDM5A (JARID1A), and PRC2 to drive heterochromatin formation [160-162]. This mechanism could have implications in repression of cryptic transcripts and may play a role in maintenance of latency when provirus is integrated into active genes. |
