PCI is a nuclear protein that is the functional equivalent of poly(ADP-ribose) polymerase-! (PARP-1; Meisterernst et al., 1997), an enzyme which is well studied for its role in DNA repair by binding to damaged DNA and in nucleic acid metabolism by covalently modifying proteins involved in these pathways and also for its involvement in the maintenance of chromatin structure (Lindahl et al., 1995; D'Amours et al., 1999). These properties of PARP-1 provide an explanation for an earlier observation that TFIIC (i.e., PARP-1) is only required for site-specific initiation of transcription by pol II when nicked DNA templates were used for in vitro transcription assays, indicating that TFIIC facilitates transcription by binding to the nicks and suppresses nonspecific initiation from damaged DNA (Slattery etal., 1983).

Mammalian PARP-1, with a molecular size of approximately 114 kDa, catalyzes the transfer of ADP-ribose units from the donor nicotinamide adenine dinucleotide (NAD+) to acceptor proteins, in a process known as poly(ADP-ribosyl)ation (Lindahl et al., 1995; D'Amours et al., 1999; Kraus and Lis, 2003). Not only does PARP-1 modify target proteins mediating DNA damage response, nucleic acid metabolism and chromatin dynamics, it also modifies transcription components, such as PC3 (i.e., DNA topoisomerase I), high mobility group protein 1 (HMG1), core histones (H2A, H2B, H3, and H4), pol II, TFIIF (RAP30 and RAP74), TBP, and p53 (Lindahl et al., 1995; Oei et al., 1998). Moreover, ADP-ribose units can be transferred to PARP-1 itself. Auto(ADP-ribosyl)ation of PARP-1 is mediated through its central domain containing multiple glutamic acid residues, which serve as acceptor sites for poly (ADP-ribosyl)ation. This central domain links the N-terminal zinc-finger DNA-binding domain to the C-terminal NAD+-binding catalytic domain (D'Amours et al, 1999; Kraus and Lis, 2003). When disrupted, as observed during apoptosis where PARP-1 is cleaved by caspase death enzymes to release a 24-kDa N-terminal DNA-binding fragment and an 89-kDa C-terminal catalytic fragment, PARP-1 typically loses its enzymatic activity. For years, PARP-1 cleavage has been used as a diagnostic marker for programmed cell death.

Unlike the well-documented roles of PARP-1 in DNA repair and apoptosis, the transcriptional role of PARP-1 has not been extensively studied. Obviously, the coactivator function of PARP-1 is mediated by its direct contact with distinct transcriptional activators, including the human T-cell leukemia virus type 1 Tax protein (Anderson et al., 2000), human papillomavirus type 18 E2 (Lee et al., 2002), B-Myb (Cervellera and

Sala, 2000), E2F-1 (Simbulan-Rosenthal et al, 2003), AP2 (Kannan et al., 1999), TEF-1 (Butler and Ordahl, 1999), and NFkB (Hassa et al., 2003). Since the C-terminal domain of PARP-1 is necessary for TEF-1-and NFicB-dependent transcription (Butler and Ordahl, 1999; Hassa et al., 2003), but appears dispensable for Gal4-AH-mediated activation (Meisterernst ei al., 1997), it seems that the catalytic activity of PARP-1 is differentially required for gene activation, depending on the specific activators and promoters involved. Using a cell-free transcription system performed with a Gal4-driven DNA template, it was shown that PARP-1 could stimulate PIC formation at a step post TFIID binding to the promoter region (Meisteremst et al., 1997). However, the exact step regulated by PARP-1 during PIC assembly has not been elucidated.

Other than the coactivating function, PARP-1 also possesses repressing activity able to inhibit transcription through different mechanisms. First, PARP-1 can be incorporated into chromatin via its N-terminal DNA-binding domain to promote formation of a highly condensed chromatin structure, thereby inhibiting activator-dependent transcription (Kim et al., 2004). Second, PARP-1 can be incorporated into a corepressor complex containing many protein components susceptible to modification by PARP-1, leading to disassembly of the corepressor complex on the target gene (Ju et al, 2004). Third, PARP-1 is capable of inhibiting ligand-dependent transcription by TRd in transient reporter gene assays in a catalytic domain-dependent manner (Miyamoto et al, 1999), suggesting that poly(ADP-ribosyl)ation of critical transcription components is likely involved in PARP-1-mediated transcriptional repression. This is consistent with the observation that poly(ADP-ribosyl)ation of sequence-specific DNA-binding proteins, such as p53, YY1, Spl, and TBP, prevents binding to their cognate sequences (Malanga et al, 1998; Oei et al, 1998; Mendoza-Alvarez and Alvarez-Gonzalez, 2001). In the case of p53, the sites for poly(ADP-ribosyl)ation have been mapped to the DNA-binding and oligomerization domains of p53 (Malanga et al, 1998). Interestingly, the enzymatic activity of PARP-1 is also critical for derepression to occur on some silenced loci, as seen by the association of PARP-1 and poly(ADP-ribosyl)ated proteins with decondensed chromatin structure at transcriptionally induced Drosophila polytene chromosome puffs (Tulin and Spradling, 2003). Clearly, PARP-1 can function as a molecular switch to convert a silenced gene into a transcriptionally active state, by first dissociating a corepressor complex via poly(ADP-ribosyl)ation (Ju et al, 2004) or by removing a CDK8 repression module from the larger Mediator complex (Pavri et al., 2005), and then enhancing activator-facilitated recruitment of chromatin-modifying enzymes, such as CBP or p300 HAT or ATP-dependent chromatin remodelers, to the targeted promoters.

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