The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse

The chemotherapeutic agent CX-5461 irreversibly blocks RNA polymerase I initiation and promoter release to cause nucleolar disruption, DNA damage and cell inviability

In the search for drugs to effectively treat cancer, the last 10 years have seen a resurgence of interest in targeting ribosome biogenesis. CX-5461 is a potential inhibitor of ribosomal RNA synthesis that is now showing promise in phase I trials as a chemotherapeutic agent for a range of malignancies. Here, we show that CX-5461 irreversibly inhibits ribosomal RNA transcription by arresting RNA polymerase I (RPI/Pol1/PolR1) in a transcription initiation complex. CX-5461 does not achieve this by preventing formation of the pre-initiation complex nor does it affect the promoter recruitment of the SL1 TBP complex or the HMGB-box upstream binding factor (UBF/UBTF). CX-5461 also does not prevent the subsequent recruitment of the initiation-competent RPI–Rrn3 complex. Rather, CX-5461 blocks promoter release of RPI–Rrn3, which remains irreversibly locked in the pre-initiation complex even after extensive drug removal. Unexpectedly, this results in an unproductive mode of RPI recruitment that correlates with the onset of nucleolar stress, inhibition of DNA replication, genome-wide DNA damage and cellular senescence. Our data demonstrate that the cytotoxicity of CX-5461 is at least in part the result of an irreversible inhibition of RPI transcription initiation and hence are of direct relevance to the design of improved strategies of chemotherapy.

Interaction of nucleolin with an evolutionarily conserved pre-ribosomal RNA sequence is required for the assembly of the primary processing complex

The first processing event of the precursor ribosomal RNA (pre-rRNA) takes place within the 5' external transcribed spacer. This primary processing requires conserved cis-acting RNA sequence downstream from the cleavage site and several nucleic acids (small nucleolar RNAs) and proteins trans-acting factors including nucleolin, a major nucleolar protein. The specific interaction of nucleolin with the pre-rRNA is required for processing in vitro. Xenopus laevis and hamster nucleolin interact with the same pre-rRNA site and stimulate the processing activity of a mouse cell extract. A highly conserved 11-nucleotide sequence located 5-6 nucleotides after the processing site is required for the interaction of nucleolin and processing. In vitro selection experiments with nucleolin have identified an RNA sequence that contains the UCGA motif present in the 11-nucleotide conserved sequence. The interaction of nucleolin with pre-rRNA is required for the formation of an active processing complex. Our findings demonstrate that nucleolin is a key factor for the assembly and maturation of pre-ribosomal ribonucleoparticles.

Nucleolin functions in the first step of ribosomal RNA processing

The first processing step of precursor ribosomal RNA (pre-rRNA) involves a cleavage within the 5' external transcribed spacer. This processing requires sequences downstream of the cleavage site which are perfectly conserved among human, mouse and Xenopus and also several small nucleolar RNAs (snoRNAs): U3, U14, U17 and E3. In this study, we show that nucleolin, one of the major RNA-binding proteins of the nucleolus, is involved in the early cleavage of pre-rRNA. Nucleolin interacts with the pre-rRNA substrate, and we demonstrate that this interaction is required for the processing reaction in vitro. Furthermore, we show that nucleolin interacts with the U3 snoRNP. Increased levels of nucleolin, in the presence of the U3 snoRNA, activate the processing activity of a S100 cell extract. Our results suggest that the interaction of nucleolin with the pre-rRNA substrate might be a limiting step in the primary processing reaction. Nucleolin is the first identified metazoan proteinaceous factor that interacts directly with the rRNA substrate and that is required for the processing reaction. Potential roles for nucleolin in the primary processing reaction and in ribosome biogenesis are discussed.

Mosaic methylation of the repeat unit of the human ribosomal RNA genes

The pattern of methylation in human genes for 18S and 28S ribosomal RNA has been investigated using methylation-sensitive restriction enzymes. We find that the transcribed region of the repeat unit is predominantly unmethylated, in agreement with previous studies. In contrast the non-transcribed spacer, which makes up the majority of the 43 kb repeat unit, is highly methylated in blood cell DNA. The boundaries between methylated and non-methylated domains appear to be relatively sharp, and occur approximately 1.5 kb upstream of the 5' edge of the proximal promoter and approximately 1.0 kb downstream of the 3' end of the transcribed region. A small proportion of all repeat units are methylated throughout the transcribed region, and may represent silent genes. The coincidence between the methylation pattern, the transcription pattern and other features of the repeat unit has implications for our understanding of the mechanism by which patterns of DNA methylation are generated.

Identification and analysis of the start site of ribosomal RNA transcription of Entamoeba histolytica

In this article we report the identification of the start site of ribosomal RNA transcription unit of the enteric parasite E. histolytica. We cloned the upstream region of the ribosomal RNA and we defined the 5' boundary of the transcription unit with nuclear run-on assays. We report that ribosomal transcription starts 2447 bp upstream the SSU ribosomal gene, at an adenosine residue. This data was supported both by S1 mapping and by primer extension analysis; that the mapped site was indeed the transcription start point was demonstrated by RNAse protection of the in vitro capped RNA. Our sequence data around the transcription start point shows two different tandem repeat clusters immediately downstream from the transcription start point.

Cloning and identification of the pig ribosomal gene promoter

Pig ribosomal RNA-encoding gene (rDNA) clones were obtained by screening a pig genomic DNA library. A 742-bp segment containing the promoter was sequenced. Using total pig RNA, the tsp (transcription start point) was defined by primer extension. A promoter-like region was found immediately upstream from the active promoter. Promoter function was studied by transfection of pig tissue culture cells and assayed by a highly sensitive RT-PCR method. Alignment of five mammalian rDNA promoter sequences, human, mouse, rat, rabbit and pig, showed five conserved subregions which may be important in transcriptional regulation. An unusual feature of the pig rDNA promoter is that instead of a G at -16, which is conserved in eukaryotes, there is a C.

Identification of a sequence-specific protein binding the 5'-transcribed spacer of rat ribosomal genes

A novel 85-kD protein factor which interacts specifically with the 5'-transcribed spacer of rat ribosomal genes was identified using the gel mobility shift, DNase I protection and UV-crosslinking techniques. The binding site of the factor is located inside the 36 bp Alul-HindIII fragment of transcribed spacer, most probably in the region +94 to +115 with respect to the transcription initiation site. Factors giving very similar gel mobility shift patterns were also found in mouse and human cell extracts. Sequences resembling the binding site of this factor were revealed in corresponding regions of mouse and human ribosomal genes. The biological function of FTS remains to be elucidated.

The structure of a gene containing introns and encoding rat ribosomal protein P2

The single rat ribosomal protein P2 gene containing introns has been characterized. It has 2275 nucleotides distributed in 5 exons and 4 introns. The sequence of amino acids encoded in the exons corresponds exactly to that derived before from a cDNA. Only this one P2 gene in a family of approximately 9 members has introns and is expressed. There are two transcriptional start sites (adjacent cytidine residues) located in a tract of 10 pyrimidines flanked by GC-rich regions. The P2 gene, like other mammalian ribosomal protein genes, lacks a TATA box; however, it has at positions -30 to -27 the sequence TTTA which may be a degenerate TATA box and may serve the same function. The architecture of the P2 gene, and especially the structure of the promoter region, resembles that of other mammalian ribosomal protein genes. This suggests that the common features contribute to the coordinate regulation of their transcription and that the stoichiometry of P2 (it is present in 2 copies in the ribosome) is achieved by regulation of the translation of its mRNA.

Platelet derived growth factor messenger RNA is increased in bone marrow megakaryocytes in patients with myeloproliferative disorders

Platelet derived growth factor (PDGF) has been suggested to play an important role in the pathogenesis of myelofibrosis, which often occurs in patients with myeloproliferative disorders (MPD). We examined the expression level of PDGF mRNA in bone marrow megakaryocytes from 13 MPD patients by in situ hybridization, using cDNA probes for both human PDGF A chain and B chain (c-sis). The mRNA level for both chains in the patients was significantly higher than that in control patients, and was markedly higher for one patient with essential thrombocythemia and one with polycythemia vera. Transcripts for A chain and B chain were expressed with a positive correlation in the MPD patients. Using the marrow fibroblast proliferation assay, we found PDGF activity in purified megakaryocytes from one of the MPD patients with high mRNA level to be similar to that from one control patient. In addition, PDGF was previously shown to be decreased in circulating platelets from MPD patients. These results may suggest that, in some patients, PDGF is synthesized in megakaryocytes at a high rate, but some fraction is released into the bone marrow environment, if the level of PDGF mRNA is assumed to be linearly related to the protein synthesized. This might be one possible mechanism causing marrow fibrosis in MPD patients.

Structural analysis of the short length ribosomal DNA variant from Pisum sativum L. cv. Alaska

The genomic clone, RRNpss1, representing the short ribosomal DNA length variant in Pisum sativum L. cv. Alaska, has been isolated and the 2859 bp intergenic spacer, along with the 25S rRNA 3' border and 18S rRNA 5' border, has been sequenced. The intergenic spacer contains nine tandem repeats, approximately 180 bp in length, which show greater than 80% sequence homology to each other. The RNA polymerase I transcription start site and a processing site, located 776 bp and 536 bp upstream of the 5' end of 18S rRNA, respectively, have been determined using S1 analysis. The region surrounding the +1 site shows strong homology between the positions -6 to +10 to the rDNA sites of initiation in radish, maize, and wheat. The sequence CATGCAAA is located 19 bp upstream of the site of initiation, and appears once within each subrepeat and twice more between the end of the subrepeat array and the site of initiation. A previously characterized HpaII site which shows developmental regulation of methylation is located 31 bp downstream of the site of initiation. Using RFLP linkage analysis, the short rDNA length variant of cv. Alaska is assigned to Chromosome 4 where it is genetically independent of the long rDNA length variant which is putatively assigned to Chromosome 7.

The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors

From previous work it was known that U3 RNA is hydrogen bonded to nucleolar 28 S to 35 S RNA and can be covalently crosslinked to RNA of greater than 28 S by irradiation in vivo with long-wave ultraviolet light in the presence of 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT psoralen). Here we use a novel sandwich blot technique to identify these large nucleolar RNA species as rRNA precursors and to map the site(s) of crosslinking in vivo. The crosslink occurs between one or more residues near the 5' end of U3 RNA and a 380 nucleotide region of the rat rRNA external transcribed spacer (ETS1). We have sequenced this region of the rat ETS and we show that it includes an RNA-processing site analogous to those previously mapped to approximately 3.5 kb upstream from the 5' end of mouse and human 18 S rRNAs.

Structural determinant of the species-specific transcription of the mouse rRNA gene promoter

Mammalian ribosomal DNA (rDNA) transcription has a certain species specificity such that, both in vivo and in vitro, human rDNA cannot be transcribed by mouse machinery and vice versa. This is due to a species-dependent transcription factor, TFID (Y. Mishima, I. Financsek, R. Kominami, and M. Muramatsu, Nucleic Acids Res. 10:6659-6670, 1982). On the basis of the information obtained from 5' and 3' substitution mutants, we prepared a chimeric gene in which the mouse sequence from positions -32 to -14 was inserted into the corresponding location of the human rDNA promoter. The chimeric gene could be transcribed by mouse extracts nearly as efficiently as the wild-type mouse promoter. The chimeric gene could also sequester transcription factor TFID at an efficiency similar to that for the mouse promoter. Partially purified mouse TFID that could not protect the human rDNA promoter against DNase I produced a clear footprint on this chimeric gene that was similar to that on mouse rDNA promoter. The basic structure of the mouse rDNA core promoter is discussed in relation to the interaction with TFID.

Overexpression and amplification of the c-myc gene in mouse tumors induced by chemicals and radiations

We examined expression of the c-myc gene by the dot blot hybridization of total cellular RNA from mouse primary tumors induced by chemicals and radiations. Expression of the c-myc gene was found to be elevated in 69 cases among 177 independently induced tumors of 12 different types. DNA from tumors overexpressing the myc gene was analyzed by Southern blotting. No case of rearrangement was detected. However, amplification of the c-myc gene was found in 7 cases of primary sarcomas. These included 4 cases out of 24 methylcholanthrene-induced sarcomas and 3 cases out of 7 alpha-tocopherol-induced sarcomas. We also analyzed 8 cases of sarcomas induced by radiations, but could not find changes in the gene structure of the c-myc gene. Thus, our data indicate tumor type specificity and agent specificity of c-myc gene amplification.

Structural determinant of the species-specific transcription of the mouse rRNA gene promoter

Mammalian ribosomal DNA (rDNA) transcription has a certain species specificity such that, both in vivo and in vitro, human rDNA cannot be transcribed by mouse machinery and vice versa. This is due to a species-dependent transcription factor, TFID (Y. Mishima, I. Financsek, R. Kominami, and M. Muramatsu, Nucleic Acids Res. 10:6659-6670, 1982). On the basis of the information obtained from 5' and 3' substitution mutants, we prepared a chimeric gene in which the mouse sequence from positions -32 to -14 was inserted into the corresponding location of the human rDNA promoter. The chimeric gene could be transcribed by mouse extracts nearly as efficiently as the wild-type mouse promoter. The chimeric gene could also sequester transcription factor TFID at an efficiency similar to that for the mouse promoter. Partially purified mouse TFID that could not protect the human rDNA promoter against DNase I produced a clear footprint on this chimeric gene that was similar to that on mouse rDNA promoter. The basic structure of the mouse rDNA core promoter is discussed in relation to the interaction with TFID.

Structure of melon rDNA and nucleotide sequence of the 17-25S spacer region

Restriction enzyme and hybridization analysis of melon nuclear DNA suggests a homogenous rDNA population with a repeat unit of 10.2 kb. Several full length Hind III rDNA repeat units were cloned and one of these is described in detail. The regions coding for 25S, 17S and 5.8S rRNAs were located by crossed-contact hybridization and R-loop mapping. Introns were not observed. The nucleotide sequence of the internal transcribed spacer and flanking regions was determined and compared with the corresponding region from rice rDNA by dot matrix analysis. In addition, the extent of gross sequence homology between cloned melon and pea rDNA units was determined by heteroduplex mapping.

Locations and contexts of sequences that hybridize to poly(dG-dT).(dC-dA) in mammalian ribosomal DNAs and two X-linked genes

Sequences located several kilobases both 5' and 3' of the stably transcribed portion of several genes hybridize to radio-labeled pure fragments of the alternating sequence poly (dG-dT) (dC-dA) ["poly(GT)"]. The genes include the ribosomal DNA of mouse, rat, and human, and also human glucose-6-phosphate dehydrogenase (G6PD) and mouse hypoxanthine-guanine phosphoribosyl transferase (HPRT). HPRT has additional hybridizing sequences in introns. Fragments that include the hybridizing sequences and up to 300 bp of adjoining DNA show perfect runs of poly(GT) (greater than 30bp) in all but the human 5' region of rDNA, which shows a somewhat different alternating purine:pyrimidine sequence, poly(GTAT) (36bp). Within 150 bp of these sequences in various instances are found a number of other sequences reported to affect DNA conformation in model systems. Most marked is an enhancement of sequences matching at least 67% to the consensus binding sequence for topoisomerase II. Two to ten-fold less of such sequences were found in other sequenced portions of the nontranscribed spacer or in the transcribed portion of rDNA. The conservation of the locations of tracts of alternating purine:pyrimidine between evolutionarily diverse species is consistent with a possible functional role for these sequences.

Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA

The human U3 ribonucleoprotein (RNP) has been analyzed to determine its protein constituents, sites of protein-RNA interaction, and RNA secondary structure. By using anti-U3 RNP antibodies and extracts prepared from HeLa cells labeled in vivo, the RNP was found to contain four nonphosphorylated proteins of 36, 30, 13, and 12.5 kilodaltons and two phosphorylated proteins of 74 and 59 kilodaltons. U3 nucleotides 72-90, 106-121, 154-166, and 190-217 must contain sites that interact with proteins since these regions are immunoprecipitated after treatment of the RNP with RNase A or T1. The secondary structure was probed with specific nucleases and by chemical modification with single-strand-specific reagents that block subsequent reverse transcription. Regions that are single stranded (and therefore potentially able to interact with a substrate RNA) include an evolutionarily conserved sequence at nucleotides 104-112 and nonconserved sequences at nucleotides 65-74, 80-84, and 88-93. Nucleotides 159-168 do not appear to be highly accessible, thus making it unlikely that this U3 sequence base pairs with sequences near the 5.8S rRNA-internal transcribed spacer II junction, as previously proposed. Alternative functions of the U3 RNP are discussed, including the possibility that U3 may participate in a processing event near the 3' end of 28S rRNA.

Primary processing of mammalian rRNA involves two adjacent cleavages and is not species specific

The primary transcript of the mouse rRNA gene is rapidly processed at nucleotide approximately +650 both in vivo and in vitro. Using run-off transcription in a mouse cell extract as well as S1 nuclease and primer extension analysis of cellular RNA, we demonstrated that this primary processing actually results in the formation of two species of downstream RNA which differ in length by approximately 6 nucleotides, indicating the existence of two closely positioned alternative processing sites. The 200-base-pair region just 3' to the mouse processing site has a striking 80% sequence homology with a region of the human rRNA external transcribed spacer, and S1 nuclease analysis of human cellular RNA has demonstrated that an analogous rRNA processing occurs at the 5' border of the homologous human region. Unlike rDNA transcriptional initiation, however, the primary rRNA processing is not highly species specific, for the transcript of a chimeric gene containing the human processing region adjacent to a mouse rDNA promoter was synthesized and correctly processed in a mouse cell extract. This result confirms that mouse and human rRNA undergo a common primary processing event which is evidently directed by sequences within the 200-base-pair conserved sequence region.

Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA

The human U3 ribonucleoprotein (RNP) has been analyzed to determine its protein constituents, sites of protein-RNA interaction, and RNA secondary structure. By using anti-U3 RNP antibodies and extracts prepared from HeLa cells labeled in vivo, the RNP was found to contain four nonphosphorylated proteins of 36, 30, 13, and 12.5 kilodaltons and two phosphorylated proteins of 74 and 59 kilodaltons. U3 nucleotides 72-90, 106-121, 154-166, and 190-217 must contain sites that interact with proteins since these regions are immunoprecipitated after treatment of the RNP with RNase A or T1. The secondary structure was probed with specific nucleases and by chemical modification with single-strand-specific reagents that block subsequent reverse transcription. Regions that are single stranded (and therefore potentially able to interact with a substrate RNA) include an evolutionarily conserved sequence at nucleotides 104-112 and nonconserved sequences at nucleotides 65-74, 80-84, and 88-93. Nucleotides 159-168 do not appear to be highly accessible, thus making it unlikely that this U3 sequence base pairs with sequences near the 5.8S rRNA-internal transcribed spacer II junction, as previously proposed. Alternative functions of the U3 RNP are discussed, including the possibility that U3 may participate in a processing event near the 3' end of 28S rRNA.

Primary processing of mammalian rRNA involves two adjacent cleavages and is not species specific

The primary transcript of the mouse rRNA gene is rapidly processed at nucleotide approximately +650 both in vivo and in vitro. Using run-off transcription in a mouse cell extract as well as S1 nuclease and primer extension analysis of cellular RNA, we demonstrated that this primary processing actually results in the formation of two species of downstream RNA which differ in length by approximately 6 nucleotides, indicating the existence of two closely positioned alternative processing sites. The 200-base-pair region just 3' to the mouse processing site has a striking 80% sequence homology with a region of the human rRNA external transcribed spacer, and S1 nuclease analysis of human cellular RNA has demonstrated that an analogous rRNA processing occurs at the 5' border of the homologous human region. Unlike rDNA transcriptional initiation, however, the primary rRNA processing is not highly species specific, for the transcript of a chimeric gene containing the human processing region adjacent to a mouse rDNA promoter was synthesized and correctly processed in a mouse cell extract. This result confirms that mouse and human rRNA undergo a common primary processing event which is evidently directed by sequences within the 200-base-pair conserved sequence region.

Transcription termination and RNA processing in the 3'-end spacer of mouse ribosomal RNA genes

The 3' termini of ribosomal RNA precursors from mouse FM3A cultured cells are mapped to eight sites within 625 bp downstream from the 3' terminus of 28 S rRNA. Three additional sites are mapped in liver RNA from C3H/He strain mice. Two of them, the sites at 570 bp and 625 bp are assumed to be termination sites in vivo, because they correspond to in vitro termination sites of RNA polymerase I, and 45 S RNAs having these 3' termini decay with kinetics distinct from others. The amount of 45 S RNA having the 3' terminus at other sites is variable among several mouse strains, despite their having the same DNA sequence in these regions. The ability to produce 3' termini in these sites seems to follow Mendel's law of inheritance. Therefore, we postulate that these nine sites are RNA processing sites which are controlled genetically.

Nucleotide sequence determining the first cleavage site in the processing of mouse precursor rRNA

The first step in the processing of 47S precursor rRNA in mouse cells is reproduced in vitro in an S-100 transcription reaction and consists of an endonucleolytic cleavage at residue +650 of the primary transcript followed by rapid degradation of the fragment upstream from residue +650. An analogous processing occurs in human rRNA. The mouse and human rRNA sequences are approximately equal to 80% conserved for 200 nucleotides on the 3' side of these processing sites, suggesting that this conserved region may be important in specifying the processing. To test this hypothesis, we constructed a systematic series of deletion mutants approaching the mouse rDNA processing region from both the 5' and 3' directions and analyzed the processing of their transcripts in vitro. The 5' boundary of the region required for processing is quite sharp and corresponds to the rRNA cleavage site at the 5' end of the conserved sequence region. The 3' boundary is more complex: The 3' deletions extending to between 250 and 130 nucleotides beyond the processing site cause about a 50% decrease in the amount of the processed RNA. A 3' deletion that extends to 109 nucleotides beyond the processing site greatly reduces the processing efficiency. Deletions to or beyond 91 nucleotides on the 3' side of the processing site virtually eliminate processing. Under altered ionic conditions, transcripts of 3' deletions extending to only 41 nucleotides beyond the processing site can still direct a low level of accurate processing. These results demonstrate that the mouse/human conserved sequence just on the 3' side of the primary rRNA processing site consists of several domains that direct and/or augment both the initial endonucleolytic cleavage and the closely coupled selective degradation of the upstream fragment that together constitute the primary rRNA processing event.

rDNA transcription and pre-rRNA processing during the differentiation of a mouse myoblast cell line

The rates of formation and processing of rRNA and transcription of rDNA were examined during the differentiation of MM14DZ mouse myoblasts into muscle fibers. Analyses of the incorporation of [3H]uridine into 18 and 28 S rRNAs and the UTP precursor pool indicate that the rate of rRNA formation is 2.3-fold higher in myoblasts as compared to muscle fibers. To determine if the rate of rRNA formation is regulated at the level of pre-rRNA processing, the labeling kinetics and steady state levels of pre-rRNAs were measured in myoblasts and fibers. These experiments suggest that the time required for and the efficiency of pre-rRNA processing are the same in myoblasts and fibers, but that the steady state levels of all pre-rRNAs detected (32, 34, 37, 41, and three 45 S subspecies) are reduced 2.5- to 3.0-fold in fibers. This suggests that the reduced rate of rRNA formation in fibers is not regulated at the level of pre-rRNA processing but is due to a decrease in the rate of rDNA transcription. The transcriptional rates for rRNA in myoblasts and fibers were calculated from measurements of the total rate of transcription and from hybridization analyses of radioactive rRNA formed in isolated nuclei or in short pulses of cultured cells. These experiments indicate that the rates of 18 and 28 S rDNA and 5 S rDNA transcription are reduced 2.5 to 3.0-fold in fibers. Thus, a coordinate change in the rate of rDNA transcription is the primary mechanism regulating the formation of rRNA during the differentiation of this myoblast line. This decreased transcription in fibers appears to be due to modulation of the activity of the known mouse rDNA promoter, as S1 nuclease mapping experiments indicate that rDNA transcription initiates at the same location in both myoblasts and fibers.

Transcription of mouse rDNA and associated formation of the nucleolus organizer region after gene transfer and amplification in Chinese hamster cells

Mouse rDNA can initiate transcription by using only Chinese hamster cell components, and this is associated with nucleolus organizer activity. To demonstrate this, we transferred a 3.2-kilobase segment of mouse rDNA containing the promoter, the transcription initiation site, and part of the external transcribed spacer to dihydrofolate reductase-deficient Chinese hamster cells by cotransformation with an abbreviated mouse dhfr gene. Stepwise selection for methotrexate resistance produced sublines in which the mouse rDNA was usually coamplified with the donor dhfr DNA and occupied the same site or sites in the hamster genome, as shown by in situ hybridization. Transcription from mouse rDNA was demonstrated in two such lines, and S1 protection mapping indicated faithful initiation of the transcript. In some cells from both lines, the chromosome segments containing amplified mouse rDNA showed multiple silver-staining regions (i.e., active nucleolus organizers). Although the transferred mouse rDNA was able to use the rDNA transcriptional machinery of the Chinese hamster, the level of transcription was much lower than expected from the rDNA copy number, and a large fraction of each amplified region showed no silver staining. Since the absence of silver staining is generally correlated with the absence of transcription, many copies of the amplified mouse rDNA may have been in a chromatin conformation in which they could not be transcribed. This was not associated with the extensive methylation seen in other amplified, inactive rDNA sequences.

Transcription of mouse rDNA and associated formation of the nucleolus organizer region after gene transfer and amplification in Chinese hamster cells

Mouse rDNA can initiate transcription by using only Chinese hamster cell components, and this is associated with nucleolus organizer activity. To demonstrate this, we transferred a 3.2-kilobase segment of mouse rDNA containing the promoter, the transcription initiation site, and part of the external transcribed spacer to dihydrofolate reductase-deficient Chinese hamster cells by cotransformation with an abbreviated mouse dhfr gene. Stepwise selection for methotrexate resistance produced sublines in which the mouse rDNA was usually coamplified with the donor dhfr DNA and occupied the same site or sites in the hamster genome, as shown by in situ hybridization. Transcription from mouse rDNA was demonstrated in two such lines, and S1 protection mapping indicated faithful initiation of the transcript. In some cells from both lines, the chromosome segments containing amplified mouse rDNA showed multiple silver-staining regions (i.e., active nucleolus organizers). Although the transferred mouse rDNA was able to use the rDNA transcriptional machinery of the Chinese hamster, the level of transcription was much lower than expected from the rDNA copy number, and a large fraction of each amplified region showed no silver staining. Since the absence of silver staining is generally correlated with the absence of transcription, many copies of the amplified mouse rDNA may have been in a chromatin conformation in which they could not be transcribed. This was not associated with the extensive methylation seen in other amplified, inactive rDNA sequences.

A complex control region of the mouse rRNA gene directs accurate initiation by RNA polymerase I

To determine the size and location of the mouse rDNA promoter, we constructed systematic series of deletion mutants approaching the initiation site from the 5' and 3' directions. These templates were transcribed in vitro under various conditions with S-100 and whole-cell extracts. Surprisingly, the size of the rDNA region that determines the level of transcription differed markedly, depending on the reaction conditions. In both kinds of cell extracts, the apparent 5' border of the promoter was at residue ca. -27 under optimal transcription conditions, but as reaction conditions became less favorable, the 5' border moved progressively out to residues -35, -39, and -45. The complete promoter, however, extends considerably further, for under other nonoptimal conditions, we observed major effects of promoter domains extending in the 5' direction to positions ca. -100 and -140. In contrast, the apparent 3' border of the mouse rDNA promoter was at residue ca. +9 under all conditions examined. We also show that the subcloned rDNA region from -39 to +9 contains sufficient information to initiate accurately and that the region between +2 and +9 can influence the specificity of initiation. These data indicate that, although the polymerase I transcription factors recognize and accurately initiate with only the sequences downstream of residue -40, sequences extending out to residue -140 greatly favor the initiation reaction; presumably, this entire region is involved in rRNA transcription in vivo.

Presence of a limited number of essential nucleotides in the promoter region of mouse ribosomal RNA gene

Point mutations are introduced into a mouse rDNA fragment containing the promoter region by a sodium bisulfite method and the mutants are tested for the ability of accurate transcription initiation in vitro. The results indicate that the change, G to A, at -7 completely eliminates the promoter activity, and those at -16 and at -25 decrease it to about 10% and 50%, respectively. On the other hand, the substitutions at +9, +4, -2, -9 and -39 do not alter the template activity significantly. It is concluded that there are limited but distinct nucleotides that are essential for the transcription initiation of this gene. This sort of absolute requirement for single specific bases is not reported in protein coding genes transcribed by RNA polymerase II. We propose that these rigid recognition signals which we have found are the molecular basis for the strong species-dependency of the transcription machinery of RNA polymerase I system. A model is presented in which a transcription factor interacts with the rDNA promoter from one side of the DNA double-helix with essential contacts at these bases.

Spacer sequences downstream of the 28S RNA coding region are part of the mouse rDNA transcription unit

Evidence is presented that more than 300 bp of spacer sequences downstream of the 28S RNA coding sequence are part of the mouse rDNA transcription unit. Studies in two cell-free transcription systems as well as analysis of cellular RNA indicate that RNA polymerase I does not terminate within the 334 bp 3' terminal spacer sequences contained in the rDNA clone used. Quantitative hybridization data, S1 mapping experiments and Northern analysis of nuclear RNA showed that the 14 kb pre-rRNA molecules hybridize with the same efficiency to both the 28S and the 3' NTS specific DNA probe. This indicates that the rRNA precursor contains both at the 5' and 3' end several hundreds bases of external transcribed spacer sequences which are eliminated in subsequent processing reactions.

Conserved arrangements of repeated DNA sequences in nontranscribed spacers of ciliate ribosomal RNA genes: evidence for molecular coevolution

We have analyzed the nucleotide sequences of the nontranscribed spacer (NTS) and transcription initiation and termination regions of the extrachromosomal rDNAs of the ciliated protozoans Tetrahymena thermophila and Glaucoma chattoni. The sequences surrounding the sites of transcription initiation and termination are highly conserved. The only extensive homologies of the NTS regions occur in five sets of dispersed repetitive sequences. Type I, II and III repeats in the 5' NTS are strongly conserved in sequence between Tetrahymena and Glaucoma in the case of the type I and III repeats, and in location relative to the transcription initiation site in the case of type I and II repeats. We identify two new repeat types, designated IV and V, in the 3' NTS. The sequence of type IV repeats, and the location relative to the transcription termination site of type IV and V repeats, are conserved. All five types of repeats are interspersed with nonconserved DNA sequences. These results suggest that the five repeat types in the 5' and 3' NTSs are important in rRNA gene function; the sequence organization, and the differing rates of divergence between species of the repeat types, provide strong evidence for their functional selection through the process of molecular coevolution.

A complex control region of the mouse rRNA gene directs accurate initiation by RNA polymerase I

To determine the size and location of the mouse rDNA promoter, we constructed systematic series of deletion mutants approaching the initiation site from the 5' and 3' directions. These templates were transcribed in vitro under various conditions with S-100 and whole-cell extracts. Surprisingly, the size of the rDNA region that determines the level of transcription differed markedly, depending on the reaction conditions. In both kinds of cell extracts, the apparent 5' border of the promoter was at residue ca. -27 under optimal transcription conditions, but as reaction conditions became less favorable, the 5' border moved progressively out to residues -35, -39, and -45. The complete promoter, however, extends considerably further, for under other nonoptimal conditions, we observed major effects of promoter domains extending in the 5' direction to positions ca. -100 and -140. In contrast, the apparent 3' border of the mouse rDNA promoter was at residue ca. +9 under all conditions examined. We also show that the subcloned rDNA region from -39 to +9 contains sufficient information to initiate accurately and that the region between +2 and +9 can influence the specificity of initiation. These data indicate that, although the polymerase I transcription factors recognize and accurately initiate with only the sequences downstream of residue -40, sequences extending out to residue -140 greatly favor the initiation reaction; presumably, this entire region is involved in rRNA transcription in vivo.

Processing of the external transcribed spacer of murine rRNA and site of action of actinomycin D

The primary rRNA transcript contains a large external transcribed spacer (ETS) approximately 4,000 nucleotides in length. We have used subcloned DNA probes derived from the 5' end of the ETS in conjunction with Northern blot analysis of murine nuclear RNA to examine processing of this region. In agreement with the results of previous investigators, we find that the large rRNA precursor lacks part of the ETS region. These ETS sequences are also missing from subsequent rRNA processing intermediates. Experiments using actinomycin D confirm that the excision of portion of the ETS is an early event in rRNA processing. In addition, in the presence of actinomycin D small RNA species accumulate which hybridize to a probe specific for the 5' end of the ETS. The length of these abbreviated transcripts defines a region of rDNA which is probably a target for this drug.

Transcription of the mouse ribosomal spacer region

This paper describes experiments designed to test the hypothesis that DNA sequences upstream from the mouse rRNA promoter are transcribed in vivo or in vitro. Plasmid pB28 contains a SalI restriction fragment that extends from -169 to -1,894 base pairs, with respect to the origin of transcription of pre-rRNA. Labeled RNA synthesized in intact cells does not hybridize to this region. Neither S1 nuclease mapping nor RNA dot blot hybridization revealed the presence of sequences complementary to this region. Transcriptional studies carried out in vitro indicated that this region is not transcribed under conditions that are optimal for utilization of the authentic rRNA promoter. Moreover, this region does not appear to form stable transcription complexes with RNA polymerase I transcription components. These data indicate that the mouse rDNA repeating unit differs from those of Xenopus spp. and Drosophila melanogaster in that reduplicated RNA polymerase I promoters are not found in the mouse rDNA spacer region.

Transcription of the mouse ribosomal spacer region

This paper describes experiments designed to test the hypothesis that DNA sequences upstream from the mouse rRNA promoter are transcribed in vivo or in vitro. Plasmid pB28 contains a SalI restriction fragment that extends from -169 to -1,894 base pairs, with respect to the origin of transcription of pre-rRNA. Labeled RNA synthesized in intact cells does not hybridize to this region. Neither S1 nuclease mapping nor RNA dot blot hybridization revealed the presence of sequences complementary to this region. Transcriptional studies carried out in vitro indicated that this region is not transcribed under conditions that are optimal for utilization of the authentic rRNA promoter. Moreover, this region does not appear to form stable transcription complexes with RNA polymerase I transcription components. These data indicate that the mouse rDNA repeating unit differs from those of Xenopus spp. and Drosophila melanogaster in that reduplicated RNA polymerase I promoters are not found in the mouse rDNA spacer region.

Glucocorticoid inhibition of initiation of transcription of the DNA encoding rRNA (rDNA) in lymphosarcoma P1798 cells

Cell-free extracts of lymphosarcoma P1798 cell culture lines support faithful initiation upon the cloned mouse DNA encoding rRNA (rDNA) promoter, whereas extracts from cells treated for 16 hr with 0.1 microM dexamethasone cannot. Extracts from both sources transcribe the cloned 5S RNA gene in vitro and mixing experiments further demonstrate that inhibition of transcription of rDNA in vitro is not due to nucleases or inhibitors of transcription present in extracts from glucocorticoid-treated cells. Incubation of extracts from control cells at 45 degrees C for 15 min inactivates RNA polymerase I and abolishes transcription. Activity can be restored by the addition of partially purified RNA polymerase I from control cells and hormone-treated cells. Moreover, extracts from hormone treated cells can be reconstituted by the addition of a partially purified, heat-stable transcription factor from control cells.

Nucleotide sequence of the 5'-terminal coding region for pre-rRNA and mature 17S rRNA in Tetrahymena thermophila rDNA

The 5'-terminus of 35S pre-rRNA and mature 17S rRNA of Tetrahymena thermophila was mapped on cloned rDNA fragments by S1 nuclease protection experiments. A single site for transcription initiation was observed when pre-rRNA prepared by three different methods was used as RNA probe. These mapping results were unambiguously confirmed by sequencing the 5'-terminal region of in vitro capped 35S pre-rRNA. DNA sequence analysis of about 520 nucleotides upstream of the transcription initiation site revealed several distinct sets of highly conserved repeat sequences. In addition, the 840 nucleotides downstream of the transcription initiation site (+ 1) was determined and shown to include the 5'-terminus of the 17S rRNA coding region at position + 647. A region surrounding the position + 195 contains an inverted repeat sequence which could be the structural basis for the recently described premature transcription termination event in this organism (Kister et al. (1983) Nucl. Acids Res. 11, 3487-3502).

Identification and sequence of the initiation site for rat 45S ribosomal RNA synthesis

The transcription initiation site for rat 45S precursor ribosomal RNA synthesis was determined by nuclease protection mapping with two single-strand endonucleases. S1 and mung bean, and one single-strand exonuclease, ExoVII. These experiments were performed with end-labeled ribosomal DNA from double-stranded pBR322 recombinants and from single-stranded M13 recombinants. Results from experiments using both kinds of DNA and all three enzymes showed that the 5' end of 45S RNA mapped to a unique site 125 bases upstream from the Hind III site in the ribosomal DNA gene. The DNA surrounding this site (designated +1) was sequenced from -281 to +641. The entire sequence of this region shows extensive homology to the comparable region of mouse. This includes three stretches of T residues in the non-coding strand between +300 and +630. Two sets of direct repeats adjacent to these T-rich regions are observed. Comparison of the mouse and human ribosomal DNA transcription initiation sites with the rat sequence reported in this paper demonstrates a conserved sequence at +2 to +16, CTGACACGCTGTCCT. This suggests that this region may be important for the initiation of transcription on mammalian ribosomal DNAs.

Independent mechanisms involved in suppression of the Moloney leukemia virus genome during differentiation of murine teratocarcinoma cells

Expression and DNA methylation of the Moloney murine leukemia virus (M-MuLV) genome were investigated in murine teratocarcinoma cells after virus infection. The newly acquired viral genome was devoid of methylation, yet its expression was repressed. The integrated viral genome in undifferentiated teratocarcinoma cells was methylated within 15 days after infection. Although 5-azacytidine decreased the level of DNA methylation, it did not activate M-MuLV in undifferentiated cells. Activation by 5-azacytidine occurred only in differentiated teratocarcinoma cells. Thus two independent mechanisms seem to regulate gene expression during the course of differentiation. The first mechanism operates in undifferentiated cells to block expression of M-MuLV and other exogeneously acquired viral genes, such as SV40 and polyoma virus, and does not depend on DNA methylation. The second mechanism relates only to differentiated cells and represses expression of genes in which DNA is methylated.

Nucleotide sequence of the genetically labile repeated elements 5' to the origin of mouse rRNA transcription

We have determined the complete nucleotide sequence of a cloned Balb/c mouse rDNA NTS fragment containing 13 tandem copies of a 135 bp subrepeating segment. This repetitious region (VrDNA) lies close to the origin of ribosomal RNA transcription. Analyses of these VrDNA subrepeats from Balb/c and a related species, Mus pahari, reveal regions of inverted repeat DNA as well as large poly T tracts, either of which may be significant to the generation of the high levels of VrDNA copy number variation found in wild and inbred mice and/or the modulation of rRNA synthesis. Unlike the highly homogeneous subrepeats in the Xenopus laevis NTS repetitious regions, the VrDNA subrepeats differ from one another on the average by about 13%. Sequence analysis and Southern hybridization studies have also shown that, unlike the Xenopus and Drosophila NTS, extensive duplications of sequences found surrounding the mouse rRNA initiation site are found neither in the VrDNA region nor 6 kb further upstream in the NTS.

Sequence organization of the ribosomal spacer of D.melanogaster

We subcloned several fragments of the rDNA nontranscribed spacer (NTS) of D.melanogaster and analysed their nucleotide sequence. The central portion contains a variable number of 240 base pair repeated sequences ending with two contiguous Alu I sites. Within every repeat there is a 42 base pair sequence perfectly homologous to the transcription initiation site from -18 to +24. Sequences homologous to the basic 240 bp repeat are present both at the end of the unique 1900 bp region downstream to the transcription termination site and within the unique region preceding the transcription initiation site up to nucleotide -140. These results are discussed in relation to the general problem of ribosomal gene units and their evolution.

Structural organization of rat ribosomal genes restriction endonuclease analysis of genomic and cloned ribosomal DNAs

Structural organization of the rat ribosomal repeating unit was studied using hybridization of blotted restriction fragments of total rat DNA with alpha-32P-labeled cDNA probe synthesized on the 18S and 28S rRNAs. A detailed restriction endonuclease map was constructed, the 18S and 28S rRNA genes mapped and the sizes of the rat ribosomal repeating units determined. Considerable site heterogeneity of rat rDNA was revealed in both nontranscribed and external transcribed spacers. Recombinant phages containing the whole set of transcribed regions and a considerable part of a nontranscribed spacer of the rDNA were selected from the rat gene library. The restriction maps of the cloned rDNA fragments are in good agreement with the map constructed by Southern's technique, add to this map and support the existence of site heterogeneity in ribosomal repeating units. Proximal to the 3'-end of the 28S rRNA gene an internally repetitive region was found, each repeating unit being equal to approx. 150 bp. The site for transcription initiation was mapped 4.0-4.5 kb upstream from the 5'-end of the 18S rRNA gene. Frequently reiterated interspersed sequences were found in the nontranscribed spacer at approx. 2-3 kb distance from both ends of the transcribed region.

Transcription initiation site of rat ribosomal DNA

The sequence of 1,100 nucleotides surrounding the transcription initiation site of a cloned rat ribosomal RNA gene (rDNA) has been determined. The location of the 5' terminus of 45S pre-rRNA was determined by S1 nuclease mapping, reverse transcriptase elongation and confirmed by in vitro capping of 45S rRNA and in vitro transcription. Two different plasmid subclones, from two separate genomic clones of rat rDNA, contained the identical sequence surrounding the transcription initiation site: -10GGAGATATAT 1GCTGACACGC TGTCCTTTTG+20. Relatively long, greater than 15 base pairs, regions of sequence homology were found when the sequences of the initiation regions of rat and mouse rDNA (Urano, Y., Kominami, R., Mishima, Y., and Muramatsu, M., Nucleic Acids Res. 8, 6043-6058, 1980) were compared. When both the rat and mouse sequences were compared to that of human rDNA (G. Wilson, personal communication) a sequence of 15 nucleotides immediately following the initiation sites were found to be preserved.

Structure and transcription of the spinach chloroplast rDNA leader region

A cloned fragment of spinach chloroplast DNA carrying 140 bp of the 16S rRNA gene and 691 bp upstream this gene has been analysed by DNA sequencing, by in vitro transcription, by S1 mapping with chloroplast RNAs and purified 16S rRNA from 30S ribosomal subunits. A tRNAVal gene has been located between the position 394 and 465. Crude chloroplast RNA polymerase has been purified by heparin sepharose chromatography of a 80 000 g supernatant from pure lysed spinach plastids and used to transcribe the cloned Bg1 II-Pvu II DNA fragment. Four in vitro transcripts of about 830, 550, 350 and 260 bases were obtained whatever RNA polymerase used: the chloroplast or the E. coli enzyme. The transcripts of 550 and 260 bases are initiated by ATP. S1 mapping with in vivo chloroplasts RNAs on 5' labelled separated strands from Bg1 II-Pvu II fragments indicates 2 protected DNA fragments respectively of 140 and 260 bases on the strand which codes for rRNAs and possibly one protected DNA fragment of 550 bases on the other strand. The start site of the 260 bases transcript might correspond to the initiation site of transcription of the rRNA genes. The possibility that the 550 bases transcription of the non coding strand for rRNA genes corresponds to the beginning of a mRNA is discussed.

Multiple Pol I initiation sequences in rDNA spacers of Drosophila melanogaster

Sequence analysis of the rDNA nontranscribed spacer (NTS) of D.melanogaster shows that it contains many regions that are perfectly homologous with the Pol I transcription initiation site. Each initiation site homology is contained within a 240 base pair repeated sequence which are organised in a tandem array terminating 140 bases pairs upstream from the transcription initiation site. We discuss the significance of these regions and the maintenance of multiple homologies against the observed high rate of spacer divergence between related Drosophila species. In addition there are two other regions of repetition in the NTS: a 90 base pair periodicity commencing 16 bases downstream from the 3' end of the 28S gene and a number of 340 base pair repeats. A similar complex of different periodicities has been described in Xenopus and may be a general feature of NTS sequences.

Fractionation and reconstitution of factors required for accurate transcription of mammalian ribosomal RNA genes: identification of a species-dependent initiation factor

Mouse and human cell extracts (S100) can support an accurate and efficient transcription initiation on homologous ribosomal RNA gene (rDNA) templates. The cell extracts were fractionated with the aid of a phosphocellulose column into four fractions (termed A, B, C and D), including one containing a major part of the RNA polymerase I activity. Various reconstitution experiments indicate that fraction D is an absolute requirement for the correct and efficient transcription initiation by RNA polymerase I on both mouse and human genes. Fraction B effectively suppresses random initiation on these templates. Fraction A appears to further enhance the transcription which takes place with fractions C and D. Although fractions A, B and C are interchangeable between mouse and human extracts, fraction D is not; i.e. initiation of transcription required the presence of a homologous fraction D for both templates. The factor(s) in fraction D, however, is not literally species-specific, since mouse D fraction is capable of supporting accurate transcription initiation on a rat rDNA template in the presence of all the other fractions from human cell extract under the conditions where human D fraction is unable to support it. We conclude from these experiments that a species-dependent factor in fraction D plays an important role in the initiation of rDNA transcription in each animal species.