Purification and characterization of a DNA polymerase beta promoter initiator element-binding transcription factor from bovine testis

YY1-binding sites provide central switch functions in the PARP-1 gene expression network

Evidence is presented for the involvement of the interplay between transcription factor Yin Yang 1 (YY1) and poly(ADP-ribose) polymerase-1 (PARP-1) in the regulation of mouse PARP-1 gene (muPARP-1) promoter activity. We identified potential YY1 binding motifs (BM) at seven positions in the muPARP-1 core-promoter (-574/+200). Binding of YY1 was observed by the electrophoretic supershift assay using anti-YY1 antibody and linearized or supercoiled forms of plasmids bearing the core promoter, as well as with 30 bp oligonucleotide probes containing the individual YY1 binding motifs and four muPARP-1 promoter fragments. We detected YY1 binding to BM1 (-587/-558), BM4 (-348/-319) and a very prominent association with BM7 (+86/+115). Inspection of BM7 reveals overlap of the muPARP-1 translation start site with the Kozak sequence and YY1 and PARP-1 recognition sites. Site-directed mutagenesis of the YY1 and PARP-1 core motifs eliminated protein binding and showed that YY1 mediates PARP-1 binding next to the Kozak sequence. Transfection experiments with a reporter gene under the control of the muPARP-1 promoter revealed that YY1 binding to BM1 and BM4 independently repressed the promoter. Mutations at these sites prevented YY1 binding, allowing for increased reporter gene activity. In PARP-1 knockout cells subjected to PARP-1 overexpression, effects similar to YY1 became apparent; over expression of YY1 and PARP-1 revealed their synergistic action. Together with our previous findings these results expand the PARP-1 autoregulatory loop principle by YY1 actions, implying rigid limitation of muPARP-1 expression. The joint actions of PARP-1 and YY1 emerge as important contributions to cell homeostasis.

A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase beta

DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though there is ample polb mRNA. Here, we report that Polb protein fails to appear at the appropriate time in development when AP endonuclease 1 (Apex), the upstream protein in BER, is knocked down. Because polb contains a Creb1 binding site, we examined whether knockdown of Apex affects creb1. Apex knockdown results in loss of Creb1 and Creb complex members but not Creb1 phosphorylation. This effect is independent of p53. Although both apex and creb1 mRNA rescue Creb1 and Polb after Apex knockdown, Apex is not a co-activator of creb1 transcription. This observation has broad significance, as similar results occur when Apex is inhibited in B cells from apex^+/− mice. These results describe a novel regulatory circuit involving Apex, Creb1 and Polb and provide a mechanism for lethality of Apex loss in higher eukaryotes.

Novel role for a sterol response element binding protein in directing spermatogenic cell-specific gene expression

Sperm are highly specialized cells, and their formation requires the synthesis of a large number of unique mRNAs. However, little is known about the transcriptional mechanisms that direct male germ cell differentiation. Sterol response element binding protein 2gc (SREBP2gc) is a spermatogenic cell-enriched isoform of the ubiquitous transcription factor SREBP2, which in somatic cells is required for homeostatic regulation of cholesterol. SREBP2gc is selectively enriched in spermatocytes and spermatids, and, due to its novel structure, its synthesis is not subject to cholesterol feedback control. This suggested that SREBP2gc has unique cell- and stage-specific functions during spermatogenesis. Here, we demonstrate that this factor activates the promoter for the spermatogenesis-related gene proacrosin in a cell-specific manner. Multiple SREBP2gc response elements were identified within the 5'-flanking and proximal promoter regions of the proacrosin promoter. Mutating these elements greatly diminished in vivo expression of this promoter in spermatogenic cells of transgenic mice. These studies define a totally new function for an SREBP as a transactivator of male germ cell-specific gene expression. We propose that SREBP2gc is part of a cadre of spermatogenic cell-enriched isoforms of ubiquitously expressed transcriptional coregulators that were specifically adapted in concert to direct differentiation of the male germ cell lineage.

DNA polymerase beta gene expression: the promoter activator CREB-1 is upregulated in Chinese hamster ovary cells by DNA alkylating agent-induced stress

The DNA alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) upregulates the level of the base excision DNA repair enzyme DNA polymerase beta (beta-pol) in several mammalian cell types. Previous studies suggested that beta-pol expression is upregulated via a transcriptional mechanism that requires: the specific cAMP response element (CRE) in the beta-pol core promoter; a phosphorylated form of CRE-binding protein-1 (CREB-1); and cellular protein kinase A activity. A large family of CRE-binding proteins, ie., the ATF/CREB factors, has been identified in various cell types. This study further examines the role of CRE-binding proteins in regulating beta-pol expression through study of Chinese hamster ovary (CHO) cells. In CHO cell nuclear extract, CREB-1 and ATF-1 are the predominant CRE-binding protein family members recognizing the CRE in the beta-pol core promoter. The concentration of CREB-1 increases strongly in CHO cells after exposure to MNNG. In contrast, the level of ATF-1 does not change after MNNG treatment. Recombinant expression of CREB-1 in CHO cells is sufficient to increase expression of the endogenous beta-pol gene, even in the absence of MNNG exposure. These results indicate that beta-pol gene expression in CHO cells can be upregulated by CREB-1 and that the activation of beta-pol gene expression in response to DNA alkylating agent exposure involves a strong increase in the level of CREB-1.

Upstream stimulating factor-1 (USF1) and USF2 bind to and activate the promoter of the adenomatous polyposis coli (APC) tumor suppressor gene

The adenomatous polyposis coli (APC) gene product is involved in cell cycle arrest and apoptosis, and loss of function is associated with the development of colorectal carcinogenesis. Although it has been demonstrated that the APC gene is inducible, its transcriptional regulation has not been elucidated. Therefore, we characterized the promoter region of the APC gene and transcription factors required for basal expression. The APC gene has a TATA-less promoter and contains consensus binding sites for Octamer, AP2, Sp1, a CAAT-box, and three nucleotide sequences for E-box A, B, and M. The E-boxes are functional in several cancer cell lines and upstream stimulating factor-1 (USF1) and USF2 interact with these sites, with a preferred sequence-specificity for the B site. Analysis of activation of the cloned APC promoter by USF1 and USF2 in transient transfection assays in HCT-116 cells demonstrated that mutation of the E-box B site completely abolished the basal promoter activity. Further, the ectopic USF1 and USF2 expression in HCT-116 cells with deletion mutations of E-box A, B, and M sites showed that these E-boxes contribute to USF1- and USF2-mediated transcriptional activation of the APC promoter, with maximum promoter activity being associated with the E-box B site. Thus, USF1 and USF2 transcription factors are critical for APC gene expression.

Kinetic analysis of Sp1-mediated transcriptional activation of the human DNA polymerase beta promoter

In the present studies, we have examined the effect of Sp1 on the activation of the human DNA polymerase beta (beta-pol), a TATA-less promoter. A HeLa cell nuclear extract (NE) based in vitro runoff transcription system of core beta-pol promoter human DNA (pbetaP8) three-step kinetic model of transcription initiation were used to describe the kinetic effect of Sp1. The results showed that distal Sp1-binding sites in the core beta-pol promoter are important for transcriptional activation of the pbetaP8 promoter. A detailed kinetic analysis showed that Sp1 stimulates the activity of the pbetaP8 promoter through distal Sp1-binding sites by increasing the amount of recruitment, instead of stimulating the apparent rate of RPc assembly (k1). There was no significant effect of Sp1 on the apparent rate of open complex (RPo) formation (k2) or on the apparent rate of promoter clearance (k3) of the pbetaP8 promoter. These studies define the kinetic mechanisms by which Sp1 may regulate the rate of transcript formation of the pbetaP8 promoter, and these results may have implications for Sp1 regulation of TATA-less promoters.

Yeast one-hybrid assay identifies YY1 as a binding factor for a proacrosin promoter element

The proacrosin gene is specifically expressed in the testis and encodes an acrosomal enzyme. Previously, footprint analyses have shown binding of nuclear extracts from testis and brain to a highly conserved 17 bp motif (F1 element: 5'-AACTTCAAAATGGCTCC/T-3') located in the proacrosin promoter. By using this DNA-element as a target in a yeast one-hybrid assay, a cDNA fragment coding for the C-terminal part of the transcription factor YY1 was isolated. The binding of YY1 to this F1 element was confirmed by immunocompetition in EMSA. Because putative YY1 binding sites were also found in the promoters of other testis-specific genes, the YY1 transcription factor could play an important role in testicular gene expression.

Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding-protein-associated factors and initiator-binding proteins

Two promoter elements, the TATA element and initiator (Inr), are capable of directing specific transcription initiation of protein-encoding genes by RNA polymerase II (RNAPII). Although binding to the TATA element by the TATA-binding protein (TBP) has been shown to be the initial recognition step in transcription complex formation in vitro, the mechanism through which the basal machinery assembles into a functional complex on TATA-less promoters is controversial. Evidence supporting numerous models of Inr-mediated transcription complex formation exists, including the nucleation of a complex by Inr-binding proteins, a component of the TFIID complex, or a specific upstream activator common to many TATA-less promoters, Sp1. Using various techniques, we have undertaken a systematic analysis of the natural TATA-less human DNA polymerase beta (beta-pol) gene promoter. Although the beta-pol promoter contains upstream Sp1 elements and a functional Inr that binds YY1, neither of these factors is essential for Inr-mediated transcription complex formation. A complex containing TBP, TFIIB, TFIIF, and RNAPII (DBPolF complex) is capable of forming on the promoter in an Inr-dependent manner. A single point mutation within the Inr that affects DBPolF complex formation diminishes beta-pol transcriptional activity.

Activation of the human DNA polymerase beta promoter by a DNA-alkylating agent through induced phosphorylation of cAMP response element-binding protein-1

Treatment of cells with the DNA-alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) induces expression of the endogenous mammalian DNA polymerase beta (beta-pol) gene and of the cloned promoter in transient expression studies. The lone cAMP response element (CRE) in the core promoter, along with functional protein kinase A, is critical for the MNNG-induced up-regulation. Recently, we described a kinetic mechanism for transcriptional regulation of the beta-pol promoter in vitro and found that CRE-binding protein (CREB) from MNNG-treated cells differentially up-regulates the promoter by stimulating formation of closed preinitiation complex (RPc). Here, using a CRE-dependent chimeric beta-pol promoter, we purified the RPc assembled with nuclear extract from MNNG-treated and control HeLa cells. Comparison of proteins in the purified RPc samples revealed that the MNNG induction is associated with a strong increase in the Ser133-phosphorylated form of recombinant CREB (CREB-1). CREB depletion of the nuclear extracts diminished transcriptional activity, and addition of purified Ser133-phosphorylated CREB-1 restored activity, whereas unphosphorylated CREB-1 did not. Addition of phosphorylated CREB-1 to the control cell extract mimicked the MNNG-induced up-regulation of transcriptional activity. These results indicate that phosphorylation of CREB-1 is the probable mechanism of activation of the beta-pol promoter after treatment of cells with the DNA-alkylating agent MNNG.