Long-term risk of second malignancy in survivors of Hodgkin's disease treated during adolescence or young adulthood

PURPOSE

To quantify the long-term risk of second primary cancers (SCs) in patients diagnosed with Hodgkin's disease (HD) during adolescence or young adulthood.

PATIENTS AND METHODS

The risk of SCs was assessed in 1,253 patients diagnosed with HD before the age of 40 years and treated in two Dutch cancer centers between 1966 and 1986. The median follow-up duration was 14.1 years.

RESULTS

In all, 137 patients developed SCs, compared with 19.4 cases expected on the basis of incidence rates in the general population (relative risk [RR] = 7.0; 95% confidence interval, 5.9 to 8.3). The 25-year actuarial risk of SC overall was 27.7%. The RR of solid tumors increased greatly with younger age at the first treatment of HD, not only for breast cancer but also for all other solid tumors, with RRs of 4.9, 6.9, and 12.7 for patients first treated at ages 31 to 39 years, 21 to 30 years, and </= 20 years, respectively. Among patients first treated at the age of 20 years or younger, the RR of developing a solid tumor before the age of 40 years was significantly greater than the RR of solid tumor development at ages 40 to 49 years (RR = 27.9 v RR = 4.2; P =.0001). Patients who received salvage chemotherapy had significantly greater risk of solid cancers other than breast cancer than did patients whose treatment was restricted to initial radiotherapy or initial combined-modality treatment (RR = 9.4 and 4.7, respectively; P =. 004).

CONCLUSION

After more than 20 years of follow-up, the risk of solid tumors is still much greater in survivors of HD than in the population at large. Reassuringly, the greatly increased risk of solid tumors in patients who were young (</= 20 years of age) at the first treatment seems to decrease as these patients grow older. Our data suggest that chemotherapy may increase the risk of solid tumors from radiotherapy.

The primary and secondary structure of yeast 26S rRNA

We present the sequence of the 26S rRNA of the yeast Saccharomyces carlsbergensis as inferred from the gene sequence. The molecule is 3393 nucleotides long and consists of 48% G+C; 30 of the 43 methyl groups can be located in the sequence. Starting from the recently proposed structure of E. coli 23S rRNA (see ref. 25) we constructed a secondary structure model for yeast 26S rRNA. This structure is composed of 7 domains closed by long-range base pairings as n the bacterial counterpart. Most domains show considerable conservation of the overall structure; unpaired regions show extended sequence homology and the base-paired regions contain many compensating base pair changes. The extra length of the yeast molecule is due to a number of insertions in most of the domains, particularly in domain II. Domain VI, which is extremely conserved, is probably part of the ribosomal A site. alpha-Sarcin, which apparently inhibits the EF-1 dependent binding of aminoacyl-tRNA, causes a cleavage between position 3025 and 3026 in a conserved loop structure, just outside domain VI. Nearly all of the located methyl groups, like in E. coli, are present in domain II, V and VI and clustered to a certain extent mainly in regions with a strongly conserved primary structure. The only three methyl groups of 26S rRNA which are introduced relatively late during the processing are found in single stranded loops in domain VI very close to positions which have been shown in E. coli 23S rRNA to be at the interface of the ribosome.

Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation

Decoding of UGA selenocysteine codons in eubacteria is mediated by the specialized elongation factor SelB, which conveys the charged tRNA(Sec) to the A site of the ribosome, through binding to the SECIS mRNA hairpin. In an attempt to isolate the eukaryotic homolog of SelB, a database search in this work identified a mouse expressed sequence tag containing the complete cDNA encoding a novel protein of 583 amino acids, which we called mSelB. Several lines of evidence enabled us to establish that mSelB is the bona fide mammalian elongation factor for selenoprotein translation: it binds GTP, recognizes the Sec-tRNA(Sec) in vitro and in vivo, and is required for efficient selenoprotein translation in vivo. In contrast to the eubacterial SelB, the recombinant mSelB alone is unable to bind specifically the eukaryotic SECIS RNA hairpin. However, complementation with HeLa cell extracts led to the formation of a SECIS-dependent complex containing mSelB and at least another factor. Therefore, the role carried out by a single elongation factor in eubacterial selenoprotein translation is devoted to two or more specialized proteins in eukaryotes.

A common octamer motif binding protein is involved in the transcription of U6 snRNA by RNA polymerase III and U2 snRNA by RNA polymerase II

The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5'-flanking sequences of the gene that are important for U6 expression are defined. Deletion of the first, between positions -156 and -280 relative to the site of transcription initiation, reduces transcription to roughly 5% of its original level. Deletion of the second, between -60 and -77, abolishes transcription. These regions contain not only functional but also sequence homology to the previously defined distal and proximal sequence elements (DSE and PSE) of the Xenopus U2 promoter, although U2 is transcribed by RNA polymerase II and U6 by RNA polymerase III. Competition experiments show that at least the distal sequence elements of the two promoters bind to a common factor both in vivo and in vitro. Part of the sequence recognized by this factor is the octamer motif (ATG-CAAAT). A sequence similar to the common RNA polymerase II TATA box is also shown to have an effect, albeit minor, on U6 transcription. The U6 coding region contains a good match to the A box, part of all previously characterized RNA polymerase III promoters. Deletion of this region has no apparent effect on the efficiency or accuracy of U6 transcription.

Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif

Selenocysteine is incorporated into selenoproteins by an in-frame UGA codon whose readthrough requires the selenocysteine insertion sequence (SECIS), a conserved hairpin in the 3'-untranslated region of eukaryotic selenoprotein mRNAs. To identify new selenoproteins, we developed a strategy that obviates the need for prior amino acid sequence information. A computational screen was used to scan nucleotide sequence data bases for sequences presenting a potential SECIS secondary structure. The computer-selected hairpins were then assayed in vivo for their functional capacities, and the cDNAs corresponding to the SECIS winners were identified. Four of them encoded novel selenoproteins as confirmed by in vivo experiments. Among these, SelZf1 and SelZf2 share a common domain with mitochondrial thioredoxin reductase-2. The three proteins, however, possess distinct N-terminal domains. We found that another protein, SelX, displays sequence similarity to a protein involved in bacterial pilus formation. For the first time, four novel selenoproteins were discovered based on a computational screen for the RNA hairpin directing selenocysteine incorporation.

Local irradiation alone for peripheral stage I lung cancer: could we omit the elective regional nodal irradiation?

PURPOSE

The results of local irradiation only for patients with Stage I lung cancer were analyzed to see whether the treatment of regional lymph nodes could be omitted.

METHODS AND MATERIALS

One hundred and eight medically inoperable patients with nonsmall cell lung cancer (T1 and peripheral T2) were treated with 60 Gy split course or 65 Gy continuous treatment. The target volume included the primary tumor only, without regional lymph nodes. Response, survival, and patterns of failure were analyzed.

RESULTS

The overall response rate was 85% with 50 (46%) complete responses (CRs). Overall survival at 3 and 5 years was 31 and 15%, and cancer-specific survival was 42 and 31% at 3 and 5 years, respectively. The actuarial 5 years local relapse free survival in patients with a CR was 52%. Tumor size (< or = 4 cm) was strongly correlated with the chance of complete remission and better survival. Of patients in complete remission, only two had a regional recurrence as the only site of relapse; an additional two patients had a locoregional recurrence.

CONCLUSION

High-dose local radiotherapy on the primary tumor only is justified for medically inoperable patients with peripherally located nonsmall lung cancer. The low regional relapse rate does not support the need for the use of large fields encompassing regional lymph nodes. Using small target volumes, higher doses can be given and better local control rates can be expected.

Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs

We determined 90% of the primary structure of E.coli MRE 600 23S rRNA by applying the sequencing gel technique to products of T1, S1, A and Naja oxiana nuclease digestion. Eight cistron heterogeneities were detected, as well as 16 differences with the published sequence of a 23S rRNA gene of an E.coli K12 strain. The positions of 13 post-transcriptionally modified nucleotides and of single-stranded, double-stranded and subunit surface regions of E.coli 23S rRNA were identified. Using these experimental results and by comparing the sequences of E.coli 23S rRNA, maize chloro. 23S rRNA and mouse and human mit 16S rRNAs, we built models of secondary structure for the two 23S rRNAs and for large portions of the two mit rRNAs. The structures proposed for maize chloroplast and E.coli 23S rRNAs are very similar, consisting of 7 domains closed by long-range base-pairings. In the mitochondrial 16S rRNAs, 3 of these domains are strongly reduced in size and have a very different primary structure compared to those of the 23S rRNAs. These domains were previously found to constitute a compact area in the E.coli 50S subunits. The conserved domains do not belong to this area and contain almost all the modified nucleotides. The most highly conserved domain, 2042-2625, is probably part of the ribosomal A site. Finally, our study strongly suggests that in cytoplasmic ribosomes the 3'-end of 5.8S rRNA is basepaired with the 5'-end of 26S rRNA. This confirms the idea that 5.8S RNA is the counterpart of the 5'-terminal region of prokaryotic 23S rRNA.

Changing the RNA polymerase specificity of U snRNA gene promoters

The promoter of a Xenopus tropicalis U6 gene can be transcribed by both RNA polymerases II and III. Two distinct elements, a TATA-like sequence and the region of transcription initiation, are only required for transcription by RNA polymerase III, while further common elements are required for transcription by both polymerases. Based on the unusually stringent requirement for a purine at the normal position of polymerase III transcription initiation and on the properties of mutants in this region, we suggest that RNA polymerase III itself may recognize the site of transcription initiation and thus be directly involved in efficient promoter selection. We have used the information obtained on U6 promoter structure to manufacture a U6 promoter that is RNA polymerase II-specific and to change the Xenopus U2 gene promoter specificity from RNA polymerase II to RNA polymerase III.

Clinical significance of bcl2 and p53 protein expression in diffuse large B-cell lymphoma: a population-based study

PURPOSE

We studied the prognostic significance of bcl2 and p53 protein expression in relation to clinical and pathologic characteristics in patients with diffuse large B-cell lymphoma (LCL).

PATIENTS AND METHODS

Three hundred seventy-two patients with LCL were retrieved from a population-based registry for non-Hodgkin's lymphoma (NHL). bcl2 and p53 protein expression was studied on paraffin-embedded tumor tissue by immunohistochemistry in relation to clinical factors. Response to therapy and survival were analyzed in 165 patients who were uniformly staged and treated and for whom all prognostic data were available according to the International Prognostic Index (IPI).

RESULTS

Forty-five percent of tumors showed strong expression of the bcl2 protein (bcl2++), with a higher frequency in patients with primary nodal involvement. Disease-free survival (DFS) was significantly better in bcl2-negative/intermediate (bcl2-/+) cases as compared with bcl2++ cases (P = .0011). At 5 years, bcl2-/+ patients showed a DFS rate of 74%, in contrast to bcl2++ patients with a DFS rate of 41% (P = .002). Bcl2 was the strongest independent prognostic value in a multivariate analysis, with a relative risk (RR) of 3.0 in comparison to p53 expression and the clinical factors of the IPI. Overall survival (OS) was not significantly influenced by bcl2 protein expression. p53 protein expression was found in 13% of cases, with a higher frequency in patients with extensive disease. p53 expression did not influence the chance to achieve complete remission (CR) and survival.

CONCLUSION

bcl2 protein is frequently expressed in LCL and is a strong independent prognostic factor for DFS. p53 expression is related with high tumor burden, but is not an independent risk factor for CR and survival.

Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man

The methods of enzymatic and chemical treatment of end-labeled RNA were applied to the determination of the nucleotide sequence of chicken and man U1A RNA and to the reexamination of that of rat U1A RNA. The chemical method allowed the easy demonstration of the cap structure. All three RNA were 165 nucleotide long. Two hitherto non described modified pyrimidines were detected close to the 5' end. Only 9 base substitutions were observed from chicken to man indicating high degree of conservation of U1A RNA through evolution.

U2 RNA shares a structural domain with U1, U4, and U5 RNAs

We previously reported common structural features within the 3'-terminal regions of U1, U4, and U5 RNAs. To check whether these features also exist in U2 RNA, the primary and secondary structures of the 3'-terminal regions of chicken, pheasant, and rat U2 RNAs were examined. Whereas no difference was observed between pheasant and chicken, the chicken and rat sequences were only 82.5% homologous. Such divergence allowed us to propose a unique model of secondary structure based on maximum base-pairing and secondary structure conservation. The same model was obtained from the results of limited digestion of U2 RNA with various nucleases. Comparison of this structure with those of U1, U4, and U5 RNAs shows that the four RNAs share a common structure designated as domain A, and consisting of a free single-stranded region with the sequence Pu-A-(U)n-G-Pup flanked by two hairpins. The hairpin on the 3' side is very stable and has the sequence Py-N-Py-Gp in the loop. The presence of this common domain is discussed in connection with relationships among U RNAs and common protein binding sites.

Acute morbidity reduction using 3DCRT for prostate carcinoma: a randomized study

PURPOSE

To study the effects on gastrointestinal and urological acute morbidity, a randomized toxicity study, comparing conventional and three-dimensional conformal radiotherapy (3DCRT) for prostate carcinoma was performed. To reveal possible volume effects, related to the observed toxicity, dose-volume histograms (DVHs) were used.

METHODS AND MATERIALS

From June 1994 to March 1996, 266 patients with prostate carcinoma, stage T1-4N0M0 were enrolled in the study. All patients were treated to a dose of 66 Gy (ICRU), using the same planning procedure, treatment technique, linear accelerator, and portal imaging procedure. However, patients in the conventional treatment arm were treated with rectangular, open fields, whereas conformal radiotherapy was performed with conformally shaped fields using a multileaf collimator. All treatment plans were made with a 3D planning system. The planning target volume (PTV) was defined to be the gross target volume (GTV) + 15 mm. Acute toxicity was evaluated using the EORTC/RTOG morbidity scoring system.

RESULTS

Patient and tumor characteristics were equally distributed between both study groups. The maximum toxicity was 57% grade 1 and 26% grade 2 gastrointestinal toxicity; 47% grade 1, 17% grade 2, and 2% grade > 2 urological toxicity. Comparing both study arms, a reduction in gastrointestinal toxicity was observed (32% and 19% grade 2 toxicity for conformal and conventional radiotherapy, respectively; p = 0.02). Further analysis revealed a marked reduction in medication for anal symptoms: this accounts for a large part of the statistical difference in gastrointestinal toxicity (18% vs. 14% [p = ns] grade 2 rectum/sigmoid toxicity and 16% vs. 8% [p < 0.0001] grade 2 anal toxicity for conventional and conformal radiotherapy, respectively). A strong correlation between exposure of the anus and anal toxicity was found, which explained the difference in anal toxicity between both study arms. No difference in urological toxicity between both treatment arms was found, despite a relatively large difference in bladder DVHs.

CONCLUSIONS

The reduction in gastrointestinal morbidity was mainly accounted for by reduced toxicity for anal symptoms using 3DCRT. The study did not show a statistically significant reduction in acute rectum/sigmoid and bladder toxicity.

Evaluation of a target contouring protocol for 3D conformal radiotherapy in non-small cell lung cancer

BACKGROUND

A protocol for the contouring of target volumes in lung cancer was implemented. Subsequently, a study was performed in order to determine the intra and inter-clinician variations in contoured volumes.

MATERIALS AND METHODS

Six radiation oncologists (RO) contoured the gross tumour volume (GTV) and/or clinical target volume (CTV), and planning target volume (PTV) for three patients with non-small cell lung cancer (NSCLC), on two separate occasions. These were, respectively, a well-circumscribed T1N0M0 lesion, an irregularly shaped T2N0M0 lesion, and a T2N2M0 tumour. Detailed diagnostic radiology reports were provided and contours were entered into a 3D planning system. The target volumes were calculated and beams-eye view (BEV) plots were generated to visualise differences in contouring. A software tool was used to expand the GTV and CTV in three dimensions for an automatically derived PTV.

RESULTS

Significant inter-RO variations in contoured target volumes were observed for all patients, and these were greater than intra-RO differences. The ratio of the largest to smallest contoured volume ranged from 1.6 for the GTV in the T1N0 lesion, to 2.0 for the PTV in the T2N2 lesion. The BEV plots revealed significant inter-RO variations in contouring the mediastinal CTV. The PTV's derived using a 3D margin programme were larger than manually contoured PTV's. These variations did not correlate with the experience of ROs.

CONCLUSIONS

Despite the use of an institutional contouring protocol, significant interclinician variations persist in contouring target volumes in NSCLC. Additional measures to decrease such variations should be incorporated into clinical trials.

An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene

H1 RNA, the RNA component of the human nuclear RNase P, is encoded by a unique gene transcribed by RNA polymerase III (Pol III). In this work, cis-acting elements and trans-acting factors involved in human H1 gene transcription were characterized by transcription assays of mutant templates and DNA binding assays of recombinant proteins. Four elements, lying within 100 bp of 5'-flanking sequences, were defined to be essential for maximal in vitro and in vivo expression, consisting of the octamer, Staf, proximal sequence element (PSE) and TATA motifs. These are also encountered in the promoter elements of vertebrate snRNA genes, where the first two constitute the distal sequence element (DSE). In all the genes examined so far, the DSE is distant from the PSE and TATA box that compose the basal promoter. However, we observed a fundamental difference in the organization of the H1 RNA and snRNA gene promoters with respect to the relative spacing of the DSE and PSE. Indeed, the H1 promoter is unusually compact, with the octamer motif and Staf binding site adjacent to the PSE and TATA motifs. It thus appears that the human RNase P RNA gene has adopted a unique promoter strategy placing the DSE immediately adjacent to the basal promoter.

Xenopus tropicalis U6 snRNA genes transcribed by Pol III contain the upstream promoter elements used by Pol II dependent U snRNA genes

We have cloned and sequenced a 977bp DNA fragment, pXTU6-2, that represents the transcription unit for a Xenopus tropicalis U6 RNA gene. This basic repeating unit is reiterated ca.500-fold per haploid genome. Oocyte injections of pXTU6-2 led to the transcription of a mature-sized U6 RNA that, however, lacked internal 2'-O-methylations. These posttranscriptional modifications of U6 RNA might be cytoplasmic and could require its association with U4 RNA to be accomplished. The low alpha- amanitin sensitivity of U6 RNA synthesis in oocytes suggested that U6 RNA is transcribed by RNA polymerase III, consistent with features of the U6 RNA molecule which also contains a Box A- like intragenic control region. Inspection of X. tropicalis, mouse and human U6 DNA upstream sequences revealed the presence of a TATA box as well as of the proximal and enhancer (octamer motif) elements contained in snRNA genes transcribed by RNA polymerase II. We propose that U6 RNAs are synthesized by a specialized transcription complex consisting of RNA polymerase III and transcription factors, some of which are very likely shared with RNA polymerase II promoters.

Selenoprotein synthesis: UGA does not end the story

It is well established that the beneficial effects of the trace element selenium are mediated by its major biological product, the amino acid selenocysteine, present in the active site of selenoproteins. These fulfill different functions, as varied as oxidation-reduction of metabolites in bacteria, reduction of reactive oxygen species, control of the redox status of the cell or thyroid hormone maturation. This review will focus on the singularities of the selenocysteine biosynthesis pathway and its unique incorporation mechanism into eukaryal selenoproteins. Selenocysteine biosynthesis from serine is achieved on tRNA(Sec) and requires four proteins. As this amino acid is encoded by an in-frame UGA codon, otherwise signaling termination of translation, ribosomes must be told not to stop at this position in the mRNA. Several molecular partners acting in cis or in trans have been identified, but their knowledge has not enabled yet to firmly establish the molecular events underlying this mechanism. Data suggest that other, so far uncharacterized factors might exist. In this survey, we attempted to compile all the data available in the literature and to describe the latest developments in the field.

The conformation of chicken, rat and human U1A RNAs in solution

Chicken, rat and human U1A RNAs in solution, were examined for secondary structure, using several methods including hydrolysis by various nucleases, hybridization to DNA oligomers and analysis of fragment interactions. The experimental results showed that the three U1A RNAs have the same structure, stable over a wide range of pH and ionic conditions. They allowed the selection of one out of several possible models constructed from the data of primary structure. This model is characterized by 4 hairpins and two single-stranded regions, the two hairpins from the 3' part of the molecule bearing very stable stems. In addition, the experimental results showed that in contrast to the 5' half of the molecule, the 3' half has a compact conformation probably stabilized by tertiary interactions. The 5' end of U1A RNA is accessible and free of base-pairing so that it might base-pair with regions of other RNA molecules, for instance, with the extremities of introns as has been recently proposed in a model of splicing.

Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III

Staf is a zinc finger protein that we recently identified as the transcriptional activator of the RNA polymerase III-transcribed selenocysteine tRNA gene. In this work we demonstrate that enhanced transcription of the majority of vertebrate snRNA and snRNA-type genes, transcribed by RNA polymerases II and III, also requires Staf. DNA binding assays and microinjection of mutant genes into Xenopus oocytes showed the presence of Staf-responsive elements in the genes for human U4C, U6, Y4 and 7SK, Xenopus U1b1, U2, U5 and MRP and mouse U6 RNAs. Using recombinant Staf, we established that it mediates the activating properties of Staf-responsive elements on RNA polymerase II and III snRNA promoters in vivo. Lastly a 19 bp consensus sequence for the Staf binding site, YY(A/T)CCC(A/G)N(A/C)AT(G/C)C(A/C)YY-RCR, was derived by binding site selection. It enabled us to identify 23 other snRNA and snRNA-type genes carrying potential Staf binding sites. Altogether, our results emphasize the prime importance of Staf as a novel activator for enhanced transcription of snRNA and snRNA-type genes.

The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes

Preparations of chicken, rat and human nuclear 5S RNA contain two sets of molecules. The set with the lowest electrophoretic mobility (5Sa) contains RNAs identical or closely related to ribosomal 5S RNA from the corresponding animal species. In HeLa cells and rat brain, we only detected an RNA identical to the ribosomal 5S RNA. In hen brain and liver, we found other species differing by a limited number of substitutions. The results suggest that mutated 5S genes may be expressed differently according to the cell type. The set with the highest mobility corresponds to U5 RNA. In both rat brain and HeLa cells, U5 RNA was found to be composed of 4 and 5 different molecules respectively (U5A, U5B1-4) differing by a small number of substitutions or insertions. In hen brain, no U5B was detected but U5A' differing from U5A by the absence of the 3'-terminal adenosine. All the U5 RNAs contain the same set of modified nucleotides. They also have the same secondary structure which consists of two hairpins joined together by a 17 nucleotide long single-stranded region. The 3' half of the molecule has a compact conformation. Together, the results suggest that U5 RNAs are transcribed from a multigene family and that mutated genes may be expressed as far as secondary structure is conserved. The conformation of U5 RNA is likely to be related to its function and it is of interest to mention that several similarities of structure are found between U5 and U1A RNA.

Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec)

Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Böck et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.

The N-terminal domain of the human TATA-binding protein plays a role in transcription from TATA-containing RNA polymerase II and III promoters

In eukaryotes, the TATA box binding protein (TBP) is an integral component of the transcription initiation complexes of all three classes of nuclear RNA polymerases. In this study we have investigated the role of the N-terminal region of human TBP in transcription initiation from RNA polymerase (Pol) I, II and III promoters by using three monoclonal antibodies (mAbs). Each antibody recognizes a distinct epitope in the N-terminal domain of human TBP. We demonstrate that these antibodies differentially affect transcription from distinct classes of promoters. One antibody, mAb1C2, and a synthetic peptide comprising its epitope selectively inhibited in vitro transcription from TATA-containing, but not from TATA-less promoters, irrespective of whether they were transcribed by Pol II or Pol III. Transcription by Pol I, on the other hand, was not affected. Two other antibodies and their respective epitope peptides did not affect transcription from any of the promoters tested. Order of addition experiments indicate that mAb1C2 did not prevent binding of TBP to the TATA box or the formation of the TBP-TFIIA-TFIIB complex but rather inhibited a subsequent step of preinitiation complex formation. These data suggest that a defined region within the N-terminal domain of human TBP may be involved in specific protein-protein interactions required for the assembly of functional preinitiation complexes on TATA-containing, but not on TATA-less promoters.

Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs

U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in addition, differs from U4A and U4B RNAs at two internal positions. Thus, U4C RNA is encoded by another gene as U4A and U4B RNAs. Only one nucleotide substitution occurred between chicken and man showing that U4A, U4B and U4C RNAs have been extremely conserved throughout evolution. The three molecular species are capped, they contain three psi, a 2'-P methyl A and a m6A. An additional post-transcriptional modification close to the cap structure is observed in man. On the basis on an experimental study, two models of secondary structure may be proposed for U4 RNA. The 3'domain is the same in both models and is homologous to that of U1 and U5 RNAs. It consists of a single-stranded region, containing the sequence Py-(A)2-(U)n-Gp flanked by two stable hairpins probably involved in tertiary interactions. The 5' domain is less stable than the 3' domain and its structure is different in the two models. However, a long single-stranded pyrimidine region containing modified nucleotides is found in both models as in U1 and U5 RNAs. Several other nucleotide sequence homologies related to specific features of secondary structure suggest that U1, U4 and U5 RNAs derive from a common ancestor and may have common function.