The promoter region of the human type-I-DNA-topoisomerase gene. Protein-binding sites and sequences involved in transcriptional regulation

The distribution of the DEK protein in mammalian chromatin

DEK is an abundant and ubiquitous chromatin protein. Here we investigate whether DEK is regularly distributed in the chromatin of human HeLa cells. We show that DEK appears to be excluded from the heterochromatic compartment. However, DEK seems to colocalize with a subfraction of chromatin bearing acetylated histone H4. We examined certain DNA sequences in specifically immunoprecipitated chromatin for four selected human genes. We found that most of the investigated gene sequences were moderately enriched in immunoprecipitated chromatin. In contrast, a promoter-proximal element of the human TOP1 gene was highly enriched in the chromatin immunoprecipitates. This enrichment was lost when cells were treated with alpha-amanitin showing that DEK binds to this particular site only when the TOP1 gene is actively expressed. Our conclusion is that DEK could serve as an architectural protein at the promoter or enhancer sites of a subfraction of human genes.

The activation of c-Jun NH2-terminal kinase (JNK) by DNA-damaging agents serves to promote drug resistance via activating transcription factor 2 (ATF2)-dependent enhanced DNA repair

The activating transcription factor 2 (ATF2) is a member of the ATF/cAMP-response element-binding protein family of basic-leucine zipper proteins involved in cellular stress response. The transcription potential of ATF2 is enhanced markedly by NH2-terminal phosphorylation by c-Jun NH2-terminal kinase (JNK) and mediates stress responses including DNA-damaging events. We have observed that four DNA-damaging agents (cisplatin, actinomycin D, MMS, and etoposide), but not the cisplatin isomer, transplatin, which does not readily damage DNA, strongly activate JNK, p38, and extracellular signal-regulated kinase (ERK), and strongly increase phosphorylation and ATF2-dependent transcriptional activity. Selective inhibition studies with PD98059, SB202190, SP600125, and the dominant negative JNK indicate that activation of JNK but not p38 kinase or ERK kinase is required for the phosphorylation and transcriptional activation of ATF2. Stable expression of ATF2 in human breast carcinoma BT474 cells increases transcriptional activity and confers resistance to the four DNA-damaging agents, but not to transplatin. Conversely, stable expression of a dominant negative ATF2 (dnATF2) quantitatively blocks phosphorylation of endogenous ATF2 leading to a marked decrease in transcriptional activity by endogenous ATF2 and a markedly increased sensitivity to the four agents as judged by decreased cell viability. Similarly, application of SB202190 at 50 micro m or SP600125 inhibited JNK activity, blocked transactivation, and sensitized parental cells to the four DNA-damaging drugs. Moreover, the wild type ATF2-expressing clones exhibited rapid DNA repair after treatment with the four DNA-damaging agents but not transplatin. Conversely, expression of dnATF2 quantitatively blocks DNA repair. These results indicate that JNK-dependent phosphorylation of ATF2 plays an important role in the drug resistance phenotype likely by mediating enhanced DNA repair by a p53-independent mechanism. JNK may be a rational target for sensitizing tumor cells to DNA-damaging chemotherapy agents.

Isolation and functional analysis of the 5'-flanking region of carrot top1beta gene coding for the beta isoform of DNA topoisomerase I

We have isolated and functionally characterized the promoter region of the top1beta gene encoding carrot (Daucus carota) DNA topoisomerase Ibeta. The major transcription start site was mapped by primer extension analysis 164 nt upstream the ATG translation start codon. Sequence analysis of the 5'-upstream region of the gene revealed the presence of a canonical TATA-like box at position -35 bp and several cis-acting sequences, including a (CT)n element in the leader region of the gene, a myb-related motif and the Dof element NtBBF-1, which correlate with the inducible expression pattern of this gene. Functional reporter analysis of the top1beta 5'-flanking region was performed in both carrot and Arabidopsis thaliana transfected protoplasts. The region at -719 to +161 was sufficient to confer high expression level in both species. The transient expression assay in protoplasts induced to stop dividing confirmed that the promoter, whose activity is low in quiescent cells, is activated when protoplasts are induced to proliferate by exogenous application of growth factors.

Regulation of gene expression, cellular localization, and in vivo function of Caenorhabditis elegans DNA topoisomerase I

BACKGROUND

DNA topoisomerase I is dispensable in yeast, but is essential during the embryogenesis of Drosophila and mouse. In order to determine functions of the enzyme in the development of Caenorhabditis elegans, phenotypes resulting from the deficiency were observed and correlated with the expression of the gene.

RESULTS

The transcriptional regulation of the C. elegans DNA topoisomerase I gene was investigated by mRNA localization and reporter gene expression in C. elegans. The mRNA was expressed in the gonad and in the early embryos, followed by a rapid decrease in its level during the late embryonic stage. A reporter gene expression induced by the 5'-upstream DNA sequence appeared at the comma stage of embryos, continued through the L1 larval stage, and began to decrease gradually afterwards. The DNA topoisomerase I protein was immuno-localized in the nuclei of meiotic gonad cells and interphase embryonic cells, and unexpectedly in centrosomes of mitotic embryonic cells. Double-stranded RNA interference of DNA topoisomerase I gene expression resulted in pleiotropic phenotypes showing abnormal gonadogenesis, oocyte development and embryogenesis.

CONCLUSION

These phenotypes, along with expressional regulations, demonstrate that DNA topoisomerase I plays important roles in rapidly growing germ cells and embryonic cells.

Characterisation of two topoisomerase 1 genes in the pufferfish (Fugu rubripes)

Eukaryotic DNA topoisomerase I manipulates the higher order structures of DNA. Only one functional topoisomerase 1 (top1) gene has previously been identified in any individual eukaryotic species. Here we report the identification and characterisation of two top1 genes in the pufferfish, Fugu rubripes. This shows that the copy number of top1, like that of other topoisomerases, may vary between eukaryotes. Both Fugu genes have 21 exons; a gene structure similar to that of human TOP1. Despite this conservation of structure, and some non-coding elements, both genes are less than a tenth of the size of the human gene. Sequence and phylogenetic analyses have shown that this duplication is ancient and also affects other species in the fish lineage.

Irinotecan in the treatment of colorectal cancer: clinical overview

PURPOSE AND METHODS

For more than three decades, the therapeutic options for patients with advanced colorectal cancer have almost exclusively been based on fluoropyrimidines. With the recognition that topoisomerase-I (TOP-I) is an important therapeutic target in cancer therapy, irinotecan, a semisynthetic TOP-I-interactive camptothecin derivative, has been clinically established in the treatment of colorectal cancer.

RESULTS

Irinotecan was investigated as second-line chemotherapy after prior treatment with fluorouracil (FU)-based regimens in two large randomized phase III trials comparing irinotecan with either best supportive care or an infusional FU/leucovorin (LV) regimen. The outcomes of these trials established irinotecan as the standard therapy in the second-line treatment of colorectal cancer. The therapeutic value of irinotecan in the first-line treatment of metastatic colorectal cancer was investigated in two large randomized phase III trials comparing the combination of irinotecan and FU/LV with FU/LV alone. Both trials demonstrated significant superior efficacy for the combination of irinotecan and FU/LV in terms of response rate, median time to disease progression, and median survival time. Consequently, the combination of irinotecan and FU/LV has been approved as first-line chemotherapy for patients with metastatic colorectal cancer and constitutes the reference therapy against which other treatment options must be tested in the future.

CONCLUSION

In this review, the clinical rationale and update of the present clinical status of irinotecan in the treatment of colorectal cancer and future prospects of irinotecan-based combinations are discussed.

Carrot cells contain two top1 genes having the coding capacity for two distinct DNA topoisomerases I

Five DNA topoisomerase I cDNA clones were isolated from a carrot (Daucus carota) cDNA library and two classes of nucleotide sequences were found. One component of the first class, pTop9, perfectly matches the open reading frame of pTop28, a truncated top1 cDNA previously described, and extended it by 594 nucleotides (top1alpha). A member of the second class, pTop11, contains an open reading frame 2727 bp long (top1ss) with a coding capacity for a second putative DNA topoisomerase I of 101 kDa. Both pTop9 and pTop11 clones are full length cDNAs. The two deduced amino acid sequences share a relevant similarity (89%) only at the C-terminal domain, whereas the similarity is reduced to 32% in the N-terminal region. Southern blot analysis and PCR amplification of genomic DNAs from carrot pure lines suggested the presence of two distinct loci. Northern blot analysis revealed the presence of two distinct transcripts of 3.0 and 3.2 kb in both cycling and starved cell populations. Three fusion peptides corresponding to the N-terminal domain of the alpha and ss forms and from the common C-terminal domain of carrot topoisomerases I were overexpressed in E. coli cells and used to raise antibodies in rabbit. Immunolocalization seems to suggest the presence of two topoisomerases I in carrot nuclei.

Inhibition of extracellular signal-regulated protein kinase or c-Jun N-terminal protein kinase cascade, differentially activated by cisplatin, sensitizes human ovarian cancer cell line

We have studied the roles of c-Jun N-terminal protein kinase (JNK) and extracellular signal-regulated protein kinase (ERK) cascade in both the cisplatin-resistant Caov-3 and the cisplatin-sensitive A2780 human ovarian cancer cell lines. Treatment of both cells with cisplatin but not transplatin isomer activates JNK and ERK. Activation of JNK by cisplatin occurred at 30 min, reached a plateau at 3 h, and declined thereafter, whereas activation of ERK by cisplatin showed a biphasic pattern, indicating the different time frame. Activation of JNK by cisplatin was maximal at 1000 microM, whereas activation of ERK was maximal at 100 microM and was less at higher concentrations, indicating the different dose dependence. Cisplatin-induced JNK activation was neither extracellular and intracellular Ca(2+)- nor protein kinase C-dependent, whereas cisplatin-induced ERK activation was extracellular and intracellular Ca(2+)- dependent and protein kinase C-dependent. A mitogen-activated protein kinase/extracellular signal-regulated kinase kinase inhibitor, PD98059, had no effect on the cisplatin-induced JNK activity, suggesting an absence of cross-talk between the ERK and JNK cascades. We further examined the effect of each cascade on the viability following cisplatin treatment. Either exogenous expression of dominant negative c-Jun or the treatment by PD98059 induced sensitivity to cisplatin in both cells. Our findings suggest that cisplatin-induced DNA damage differentially activates JNK and ERK cascades and that inhibition of either of these cascades sensitizes ovarian cancer cells to cisplatin.

DNA topoisomerase I in oncology: Dr Jekyll or Mr Hyde?

Mammalian DNA topoisomerase I is a multifunctional enzyme which is essential for embryonal development. In addition to its classical DNA nicking-closing activities which are needed for relaxation of supercoiled DNA, topoisomerase I can phosphorylate certain splicing factors. The enzyme is also involved in transcriptional regulation through its ability to associate with other proteins in the TFIID-, and possibly TFIIH-, transcription complexes, and is implicated in the recognition of DNA lesions. Finally, topoisomerase I is a recombinase which can mediate illegitimate recombination. A crucial reaction intermediate during relaxation of DNA is the formation of a DNA-topoisomerase I complex (the cleavable complex) where topoisomerase I is covalently linked to a 3 -end of DNA thereby creating a single stranded DNA break. Cleavable complexes are also formed in the vicinity of DNA lesions and in the presence of the antitumor agent, camptothecin. While formation of cleavable complexes may be necessary for the initial stages of the DNA damage response, these complexes are also potentially dangerous to the cell due to their ability to mediate illegitimate recombination, which can lead to genomic instability and oncogenesis. Thus the levels and stability of these complexes have to be strictly regulated. This is obtained by maintaining the enzyme levels relatively constant, by limiting the stability of the cleavable complexes through physical interaction with the oncogene suppressor protein p53 and by degradation of the topoisomerase I by the proteasome system. Emerging evidence suggest that these regulatory functions are perturbed in tumor cells, explaining at the same time why topoisomerase I activities so often are increased in certain human tumors, and why these cells are sensitized to the cytotoxic effects of camptothecins.

Mechanism of action of eukaryotic DNA topoisomerase I and drugs targeted to the enzyme

DNA topoisomerase I is essential for cellular metabolism and survival. It is also the target of a novel class of anticancer drugs active against previously refractory solid tumors, the camptothecins. The present review describes the topoisomerase I catalytic mechanisms with particular emphasis on the cleavage complex that represents the enzyme's catalytic intermediate and the site of action for camptothecins. Roles of topoisomerase I in DNA replication, transcription and recombination are also reviewed. Because of the importance of topoisomerase I as a chemotherapeutic target, we review the mechanisms of action of camptothecins and the other topoisomerase I inhibitors identified to date.

Alternative splicing in the Caenorhabditis elegans DNA topoisomerase I gene

5'-end cDNA fragments of the Caenorhabditis elegans DNA topoisomerase I gene were obtained by rapid amplification of the cDNA ends from C. elegans mRNAs. The presence of a SL1 sequence at the 5'-terminus of the cDNA sequence suggested trans-splicing of the pre-mRNA. By comparing the complete cDNA sequence with the genomic lambda DNA clones, the gene structure composed of five exons was established. Alternative splicing deleting the second exon was observed in the cDNA fragments obtained by a gene-specific reverse transcription followed by polymerase chain reactions. The shorter mRNA missing the second exon was expressed at all the developmental stages, while the full-length mRNA was present only in embryos.

The Jun kinase/stress-activated protein kinase pathway functions to regulate DNA repair and inhibition of the pathway sensitizes tumor cells to cisplatin

We have studied the role of Jun/stress-activated protein kinase (JNK/SAPK) pathway in DNA repair and cisplatin resistance in T98G glioblastoma cells. JUN/SAPK is activated by DNA damage and phosphorylates serines 63 and 73 in the N-terminal domain of c-Jun, which is known to increase its transactivation properties. We show that treatment of T98G glioblastoma cells with cisplatin but not the transplatin isomer activates JNK/SAPK about 10-fold. T98G cells, which are highly resistent to cisplatin (IC50 = 140 +/- 13 microM), modified to express a nonphosphorylatable dominant negative c-Jun (termed dnJun) exhibit decreased viability following treatment with cisplatin, but not transplatin, in proportion (rPearson = 0.98) to the level of dnJun expressed leading to a 7-fold decreased IC50. Similar effects are observed in U87 cells, PC-3 cells, and MCF-7 cells, as well as in T98G cells modified to express TAM-67, a known inhibitor of c-Jun function. In contrast, no sensitization effect was observed in cells modified to express wild-type c-Jun. Furthermore, through quantitative polymerase chain reaction-stop assays, we show that dnJun expressing cells were inhibited in repair of cisplatin adducts (p = 0.55), whereas repair is readily detectable (p = 0.003) in parental cells. These observations indicate that the JNK/SAPK pathway is activated by cisplatin-induced DNA damage and that this response is required for DNA repair and viability following cisplatin treatment. Regulation of DNA repair following genotoxic stress may be a normal physiological role of the JNK/SAPK pathway.

The human topoisomerase I gene promoter is regulated by NF-IL6

We investigated the expression of the human DNA topoisomerase I (hTOP1) gene in HeLa cells and in adenovirus-transformed 293 cells. A highly conserved proximal promoter element is essential for hTOP1 promoter activity in HeLa cells but not in 293 cells. This correlates with the presence of specific promoter-binding proteins in HeLa cells and their absence in 293 cells. We identified the HeLa binding protein by screening a cDNA expression library with the specific promoter site as a probe and demonstrate now that the activating protein is identical to the nuclear factor for interleukin-6 expression (NF-IL6), a member of the C/EBP family of transcription factors. Overexpression of NF-IL6 strongly stimulates hTOP1 promoter activity in HeLa cells, suggesting that NF-IL6 is a major hTOP1-regulating protein. Because of the presence of adenovirus protein E1A, 293 cells express the hTOP1 gene more efficiently than HeLa cells but do not contain NF-IL6 activity. E1A activation of the hTOP1 promoter is suppressed by NF-IL6 overexpression. This result supports previous observations concerning a functional interaction between viral protein E1A and NF-IL6. Finally, we show that hTOP1 gene expression in differentiating macrophages is correlated with the synthesis of NF-IL6-specific mRNA.

Molecular and functional interactions of transcription factor USF with the long terminal repeat of human immunodeficiency virus type 1

The human transcription factor USF, purified from HeLa cells, and its recombinant 43-kDa component bind to the long terminal repeat (LTR) of human immunodeficiency virus type 1. The proteins footprint over nucleotides from position -173 to -157 upstream of the transcription start site, generating strong DNAse I hypersensitivity sites at the 3' sides on both strands. As detected by methylation protection studies, the factor forms symmetric contacts with the guanines of the palindromic CACGTG core of the recognized sequence. Its binding ability is abolished by the mutation of this core sequence and is strongly reduced by the cytosine methylation of the central CpG dinucleotide. Upon binding, both recombinant and purified USFs bend the LTR DNA template. The role of USF in the control of transcription initiation from the LTR was tested by in vitro transcription assays. Upon addition of the protein, transcription from constructs containing an intact binding site is increased, while the responsiveness in constructs with a mutated sequence is abolished. Furthermore, the addition of a decoy plasmid which contains multiple repeats of the target sequence results in downregulation of transcription from the LTR. These results suggest that USF is a positive regulator of LTR-mediated transcriptional activation.

Transcription factor Oct1 binds to the AT-rich segment of the simian virus 40 replication origin

A cellular protein that binds to the AT-rich late segment of the simian virus 40 (SV40) origin of replication has been identified as transcription factor Oct1. This conclusion is based on the following observations: the late origin binding protein has a molecular mass of about 100 kDa, like factor Oct1, and shares other biochemical properties with Oct1; its binding to the origin is inhibited by antibodies directed against the POU domain of factor Oct1; the isolated POU domain of Oct1 specifically binds to the SV40 late origin region. Thus, the SV40 genome contains binding sites for transcription factor Oct1 in the origin of replication in addition to the previously characterized octamer sites in the viral promoter enhancer. Oct1, bound to the viral origin, negatively affects the DNA unwinding reaction catalyzed by the viral replication initiator T antigen, suggesting that Oct1 may have a role in the regulation of viral replication.

Conserved regulatory elements in the type I DNA topoisomerase gene promoters of mouse and man

The gene for mammalian type I DNA topoisomerase is constitutively expressed, but also regulated by a number of external stimuli. We compared the nucleotide sequences of the human and the mouse topoisomerase I gene promoters because promoter elements, essential for basic as well as regulated gene expression, should be conserved during evolution. We found that proximal upstream sequences are highly conserved and include potential binding sites for ubiquitous transcription factors, a regulatory CRE site as well as two novel promoter elements that have been shown to be important for the expression of the human gene. The more distal parts of the upstream sequences are less well conserved but include two regions that are almost identical in the human and the mouse gene. One of these regions contains a binding site for a basic-helix-loop-helix/leucine-zipper protein, and the other contains an AT-rich element with the potential for DNA bending.