The roles of PARP1 in gene control and cell differentiation
Introduction
Poly(ADP-ribose) polymerase 1 (PARP1) is a multifunctional nuclear protein created by eukaryotes to manage the structure and function of high order chromatin. The PARP1 protein, which is conserved among eukaryotes [1] except in yeast [2], utilizes NAD+ as substrate to synthesize poly(ADP-ribose) polymer (pADPr) with the resulting sizes varying from 2 to 200 ADP-ribose units [3]. The mammalian genome contains additional PARP superfamily members, PARP2–PARP17 [4], while the Drosophila genome encodes only two PARP superfamily members: a single nuclear PARP1 and a single cytoplasmic PARP5 (Tankyrase) [5]. PARP1 can modify target proteins by essentially attaching a poly(ADP-ribose) (pADPr) chain to itself through Glu/Asp [6] and/or lysine residues [7] in its automodification domain (Figure 1a). It is this accumulation of pADPr which leads to local chromatin loosening [8••, 9] and facilitates transcription by RNA polymerase II (Pol2) (Figure 1b). Although automodified PARP1 (pADPr-PARP1) loses its enzymatic capabilities in this process, it gains the ability to bind proteins through conserved pADPr-binding domains in a noncovalent manner [10, 11, 12] to further modulate chromatin [13••, 14••] and regulate RNA maturation steps [15••, 16•]. An antagonist of PARP1, poly(ADP-ribose) glycohydrolase (PARG), degrades the pADPr polymer and regulates the level of poly(ADP-ribosyl)ated proteins within chromatin and nucleoplasm [17, 18] (Figure 1b). In this review, we focus on recent studies of PARP1 functions under normal physiological condition and explain how nuclei can utilize the ability of PARP1 protein to modulate chromatin for transcription and splicing control during development.
Section snippets
PARP1 as the chromatin protein for transcription inhibition
In steady-state conditions, most PARP1 proteins are associated with chromatin and are accumulated in nucleoli [8••, 9, 19]. Numerous studies suggest that PARP1 binds to the core histone proteins (H2A, H2B, H3 and H4) in the nucleosome [20, 21]. Specifically, the C-terminal domain of PARP1 preferentially interacts with H3 and H4, an event not mediated by DNA but negatively regulated by the N-terminal domain of PARP1 [20]. In contrast, PARP1 and H1 compete with each other for binding to the
Interaction of activated PARP1 with histones for chromatin modulation
Many environmental and developmental signals can activate PARP1 during an organism's development. Because poly(ADP-ribose) is highly negatively charged and has a high binding affinity for its associated proteins [29], automodifed PARP1 and subsequent interactions with histones and their variants dramatically change the structure of chromatin from a condensed state to a less concentrated (i.e. ‘loose’) state which facilitates gene transcription (Figure 2). Chromatin remodeling by PARP1
Poly(ADP-ribosyl)ation of chromatin-remodeling factors for chromatin modulation
PARP1 can also modify several chromatin-remodeling factors, including Spt16 in the FACT (facilitates chromatin transcription) complex [33•, 34•] and the nucleosome-remodeling ATPases, ISWI [35••] and ALC1 (amplified in liver cancer 1) [14••, 36]. The FACT complex, a heterodimer of hSpt16 and SSRP1, is associated with the nucleosome and facilitates transcription elongation by removing one H2A–H2B dimer to enable the passage of pol II through the chromatin [37]. Upon DNA damage,
Poly(ADP-ribosyl)ation of the splicing proteins for splicing regulation
In addition to its direct effects on chromatin and transcription, as described above, PARP1 also mediates the follow-up steps of gene expression via regulation of proteins involved in RNA processing. Alternative splicing is used extensively to produce the different mRNA isoforms of a gene to increase the complexity of the transcriptome in higher eukaryotic genomes. It is generally believed that two groups of RNA-binding proteins, hnRNPs and serine-arginine-rich (SR) splicing factor, regulate
PARP1 controls developmental processes
Drosophila PARP1 loss-of-function has caused larval lethality [5], and mouse PARP1 and PARP2 double knockout mice died at the early embryonic stages [45], suggesting that poly(ADP-ribosyl)ation is essential for normal development. Although PARP1 is constitutively expressed, its enzyme activity is developmentally regulated. For example, the maximal accumulation of pADPr was observed at the prepupal stage in Drosophila [46]. Both exogenous stimuli, such as heat shock [8••], and endogenous
PARP1 controls metamorphosis in Drosophila
The developmental roles of PARP1 were illustrated in the observation that PARP1 enzymatic activity is required for chromatin loosening on ecdysone-inducible loci (E74 and E75) in Drosophila [8••]. At the end of the wandering third larval stage in Drosophila, a pulse of ecdysone triggers puparium formation and the onset of metamorphosis by inducing the expression of E74, E75 and BR-C genes [48]. The transcriptional activation is achieved by ecdysone binding to a heterodimer of two nuclear
PARPs in germline development
PARPs also play roles in germline development, including oogenesis and spermiogenesis. During meiosis, it appears that PARP1 had dynamic localization patterns in mouse oocytes, which correlates with transcription state [53•]. PARP1 null oocytes showed meiotic defects, including persistent H2AX phosphorylation, suggesting a role of PARP1 for chromatin modification during ooctye maturation [53•]. Because of the redundant function of PARP1 with PARP2, PARP1 null female mice are fertile [53•], but
PARP1 in cell differentiation
A number of studies have also demonstrated that PARP1 and poly(ADP-ribosyl)ation are involved in cell differentiation. After injection into nude mice, parp−/− embryonic stem (ES) cells can differentiate to form teratocarcinoma-like tumors with the characteristics of trophoblast giant cells, suggesting that PARP1 may inhibit ES cell differentiation into trophoectodermal cells in the wild type [55]. However, a recent study showed that PARP1, whose activity is upregulated during ES cell
Summary
PARP1 performs a dual function in transcription control. First, as the essential component of chromatin, PARP1 represses transcription locally in euchromatin and more globally in the heterochromatin. Second, once activated by developmental cues, automodified PARP1 interacts with histone H3 and H4 and their variants, such as macroH2A1, to destabilize chromatin structure in order to allow the transcription machinery to operate. In addition, activated PARP1 also poly(ADP-ribosyl)ates several
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
We thank Dr Hua-Ying Fan for her critical reading of the manuscript and valuable comments. The expenses were defrayed by a grant from the National Institutes of Health (R01DK082623) (to AVT).
References (56)
- et al.
Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins
J Biol Chem
(2000) - et al.
The macro domain is an ADP-ribose binding module
EMBO J
(2005) - et al.
Nucleosomal core histones mediate dynamic regulation of poly(ADP-ribose) polymerase 1 protein binding to chromatin and induction of its enzymatic activity
J Biol Chem
(2007) - et al.
Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, macroH2A, and contributes to silencing of the inactive X chromosome
J Biol Chem
(2007) - et al.
Structural characterization of the histone variant macroH2A
Mol Cell Biol
(2005) - et al.
Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler
Proc Natl Acad Sci U S A
(2009) - et al.
A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly(ADP-ribose)-binding proteins
Biochem J
(2003) - et al.
The Drosophila E74 gene is required for metamorphosis and plays a role in the polytene chromosome puffing response to ecdysone
Development
(1995) - et al.
Persistence of histone H2AX phosphorylation after meiotic chromosome synapsis and abnormal centromere cohesion in poly (ADP-ribose) polymerase (Parp-1) null oocytes
Dev Biol
(2009) - et al.
Poly(ADP-ribose) polymerase-2 contributes to the fidelity of male meiosis I and spermiogenesis
Proc Natl Acad Sci U S A
(2006)