Nucleosome-binding proteins act to modulate the promoter chromatin architecture and transcription of target genes. We used genomic and gene-specific approaches to show that two such factors, histone H1 and poly(ADP-ribose) polymerase-1 (PARP-1), exhibit a reciprocal pattern of chromatin binding at many RNA polymerase II-transcribed promoters. PARP-1 was enriched and H1 was depleted at these promoters. This pattern of binding was associated with actively transcribed genes. Furthermore, we showed that PARP-1 acts to exclude H1 from a subset of PARP-1-stimulated promoters, suggesting a functional interplay between PARP-1 and H1 at the level of nucleosome binding. Thus, although H1 and PARP-1 have similar nucleosome-binding properties and effects on chromatin structure in vitro, they have distinct roles in determining gene expression outcomes in vivo.

In mammals, nicotinamide phosphoribosyltransferase (NAMPT) and nicotinamide mononucleotide adenylyltransferase 1 (NMNAT-1) constitute a nuclear NAD ؉ salvage pathway which regulates the functions of NAD ؉ -dependent enzymes such as the protein deacetylase SIRT1. One of the major functions of SIRT1 is to regulate target gene transcription through modification of chromatin-associated proteins. However, little is known about the molecular mechanisms by which NAD ؉ biosynthetic enzymes regulate SIRT1 activity to control gene transcription in the nucleus. In this study we show that stable short hairpin RNA-mediated knockdown of NAMPT or NMNAT-1 in MCF-7 breast cancer cells reduces total cellular NAD ؉ levels and alters global patterns of gene expression. Furthermore, we show that SIRT1 plays a key role in mediating the gene regulatory effects of NAMPT and NMNAT-1. Specifically, we found that SIRT1 binds to the promoters of genes commonly regulated by NAMPT, NMNAT-1, and SIRT1 and that SIRT1 histone deacetylase activity is regulated by NAMPT and NMNAT-1 at these promoters. Most significantly, NMNAT-1 interacts with, and is recruited to target gene promoters by SIRT1. Collectively, our results reveal a mechanism for the direct control of SIRT1 deacetylase activity at a set of target gene promoters by NMNAT-1. This mechanism, in collaboration with NAMPT-dependent regulation of nuclear NAD ؉ production, establishes an important pathway for transcription regulation by NAD ؉ .Nicotinamide adenine dinucleotide (NAD ϩ ), a coenzyme in metabolic processes and redox reactions, is an important signaling molecule. NAD ϩ is (i) a substrate for mono-and poly-ADP-ribosylation of proteins, (ii) required for NAD ϩ -dependent protein deacetylation, and (iii) a precursor for calcium mobilizing agents (1). As a signaling molecule, NAD ϩ is consumed as a donor of ADP-ribose, releasing nicotinamide (NAM) 2 as a byproduct. Consequently, resynthesis of NAD ϩ is crucial for maintaining the functions of a wide variety of NAD ϩ -dependent enzymes in the cytoplasm and nucleus. In mammalian cells the enzymes nicotinamide phosphoribosyltransferase (NAMPT) and nicotinamide mononucleotide adenylyltransferase (NMNAT) constitute an NAD ϩ salvage/ recycling pathway using NAM as the precursor (see Fig. 1A) (2). NAMPT, a unique enzyme encoded by a single gene, catalyzes the conversion of NAM to nicotinamide mononucleotide (NMN). NAMPT localizes to both the cytosol and nucleus (3, 4).3 Interestingly, an extracellular form of NAMPT has also been described, although controversy exists regarding its function (5, 6). NMN produced by NAMPT is further converted into NAD ϩ by NMNAT. Three NMNAT enzymes encoded by distinct genes are found in mammals (7-10). Among them, NMNAT-1 is localized exclusively in the nucleus, whereas NMNAT-2 and NMNAT-3 are found in the Golgi and mitochondria, respectively (11). In the nucleus, NAMPT and NMNAT-1 form a nuclear NAD ϩ salvage pathway that supplies NAD ϩ as a substrate for a variety of NAD ϩ -dependent enzymes, including th...

Poly(ADP-ribose) polymerase-1 (PARP-1) and poly(ADPribose) glycohydrolase (PARG) are enzymes that modify target proteins by the addition and removal, respectively, of ADP-ribose polymers. Although a role for PARP-1 in gene regulation has been well established, the role of PARG is less clear. To investigate how PARP-1 and PARG coordinately regulate global patterns of gene expression, we used short hairpin RNAs to stably knock down PARP-1 or PARG in MCF-7 cells followed by expression microarray analyses. Correlation analyses showed that the majority of genes affected by the knockdown of one factor were similarly affected by the knockdown of the other factor. The most robustly regulated common genes were enriched for stress-response and metabolic functions. In chromatin immunoprecipitation assays, PARP-1 and PARG localized to the promoters of positively and negatively regulated target genes. The levels of chromatin-bound PARG at a given promoter generally correlated with the levels of PARP-1 across the subset of promoters tested. For about half of the genes tested, the binding of PARP-1 at the promoter was dependent on the binding of PARG. Experiments using stable re-expression of short hairpin RNA-resistant catalytic mutants showed that PARP-1 and PARG enzymatic activities are required for some, but not all, target genes. Collectively, our results indicate that PARP-1 and PARG, nuclear enzymes with opposing enzymatic activities, localize to target promoters and act in a similar, rather than antagonistic, manner to regulate gene expression.

Background: NAD ϩ is required for nuclear enzymes that regulate chromatin and gene expression.

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