In the postgenome era, attention is being focused on those epigenetic modifications that modulate chromatin structure to guarantee that information present on DNA is read correctly and at the most appropriate time to meet cellular requirements. Data reviewed show that along the chain of events that induce DNA methylation-dependent chromatin condensation/decondensation, a postsynthetic modification other than histone acetylation, phosphorylation, and methylation--namely poly(ADP-ribosyl)ation (PARylation)--participates in the establishment and maintenance of a genome methylation pattern. We hypothesize that the right nuclear balance between unmodified and PARylated poly(ADP-ribose) polymerase 1 (PARP-1), which depends on the dynamics of PARPs/PARG activity, is key to maintaining genomic methylation pattern. According to our data, decreased or increased levels of PARylated PARP-1 are responsible for diffuse hypermethylation or hypomethylation of DNA, respectively. In our model, polymers present on PARP-1 interact noncovalently with DNA methyltransferase 1 (Dnmt1), preventing its enzymatic activity. In the absence of PARylated PARP-1, Dnmt1 is free to methylate DNA; if, in contrast, high levels of PARylated PARP-1 persist, Dnmt1 will be stably inhibited, preventing DNA methylation.
Our previous data have shown that in L929 mouse fibroblasts the control of methylation pattern depends in part on poly(ADP-ribosyl)ation and that ADP-ribose polymers (PARs), both present on poly(ADP-ribosyl)ated PARP-1 and/or protein-free, have an inhibitory effect on Dnmt1 activity. Here we show that transient ectopic overexpression of CCCTC-binding factor (CTCF) induces PAR accumulation, PARP-1, and CTCF poly(ADP-ribosyl)ation in the same mouse fibroblasts. The persistence in time of a high PAR level affects the DNA methylation machinery; the DNA methyltransferase activity is inhibited with consequences for the methylation state of genome, which becomes diffusely hypomethylated affecting centromeric minor satellite and B1 DNA repeats. In vitro data show that CTCF is able to activate PARP-1 automodification even in the absence of nicked DNA. Our new finding that CTCF is able per se to activate PARP-1 automodification in vitro is of great interest as so far a burst of poly(ADP-ribosyl)ated PARP-1 has generally been found following introduction of DNA strand breaks. CTCF is unable to inhibit DNMT1 activity, whereas poly(ADP-ribosyl)ated PARP-1 plays this inhibitory role. These data suggest that CTCF is involved in the cross-talk between poly(ADP-ribosyl)ation and DNA methylation and underscore the importance of a rapid reversal of PARP activity, as DNA methylation pattern is responsible for an important epigenetic code.Over the past decade our laboratory accumulated evidence that links poly(ADP-ribosyl)ation with DNA methylation. A series of different experimental strategies suggests that blockage of poly-(ADP-ribosyl)ation induces in vivo DNA hypermethylation. Previous data showed that inhibition of PARP 6 activity introduces an anomalous hypermethylated pattern in genomic DNA (1, 2) and in some CpG island regions (3), suggesting that in the absence of ADP-ribose polymers some DNA regions are no longer protected from methylation. Further experiments showed that PARP activity can also affect the methylation pattern of transfected foreign DNA (4). The combined results of these different experimental approaches allowed us to propose the first method to induce DNA hypermethylation in vivo by treatment of cells in culture with PARP activity inhibitors (5) and to study by atomic force microscopy the effect of the addition of new methyl groups to DNA on chromatin structure in vivo (6).To provide an explanation for how ADP-ribose polymers control and/or protect DNA methylation patterns, several experimental approaches were used. A mechanism has been suggested in which PARP-1 in its poly(ADP-ribosyl)ated isoform makes DNMT1 catalytically inactive and, thus, inefficient in DNA methylation (7). In this model modified PARP-1 is considered as a molecular adaptor of high negative charge onto which chromatin proteins can be attracted and hosted (8). Several proteins show a greater affinity for ADP-ribose polymers than for DNA (9), so that these polymers compete with DNA for binding of these proteins (10). This noncovalent link...
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