E6 RNA Research Articles

Three small nucleolar RNAs that are involved in ribosomal RNA precursor processing.

Three small nucleolar RNAs (snoRNAs), E1, E2 and E3, have been described that have unique sequences and interact directly with unique segments of pre-rRNA in vivo. In this report, injection of antisense oligodeoxynucleotides into Xenopus laevis oocytes was used to target the specific degradation of these snoRNAs. Specific disruptions of pre-rRNA processing were then observed, which were reversed by injection of the corresponding in vitro-synthesized snoRNA. Degradation of each of these three snoRNAs produced a unique rRNA maturation phenotype. E1 RNA depletion shut down 18 rRNA formation, without overaccumulation of 20S pre-rRNA. After E2 RNA degradation, production of 18S rRNA and 36S pre-rRNA stopped, and 38S pre-rRNA accumulated, without overaccumulation of 20S pre-rRNA. E3 RNA depletion induced the accumulation of 36S pre-rRNA. This suggests that each of these snoRNAs plays a different role in pre-rRNA processing and indicates that E1 and E2 RNAs are essential for 18S rRNA formation. The available data support the proposal that these snoRNAs are at least involved in pre-rRNA processing at the following pre-rRNA cleavage sites: E1 at the 5' end and E2 at the 3' end of 18S rRNA, and E3 at or near the 5' end of 5.8S rRNA.

Identification and location of human papillomavirus type 16 antisense early promoter and characterisation of antisense RNA.

Antisense RNA sequences of various regions of human papillomavirus type 16 (HPV 16) were previously found in a number of cervical lesions, but the viral or cellular promoter has not been identified. HPV 16 E7 oncogene antisense transcripts expressed from an antisense promoter in viral DNA were found in the present study by RNase protection assays for total and cytoplasmic RNA. The antisense promoter for these transcripts was located within HPV 16 nt 4030-4230 by deletion analyses. The results also suggested that most of the antisense RNA was relatively short. The antisense promoter of HPV 16 was functional for expression of antisense RNA of a heterologous gene. Antisense-sense double-stranded E7 RNA was detected, and the sense RNA of this duplex was apparently inefficient for splicing or cleavage/poly(A) addition. These results show that HPV 16 can produce early region antisense RNA, which is from a promoter within a defined region of the viral genome. The possible importance of these transcripts for the regulation of episomal HPV 16 gene expression in infected and premalignant lesions and the possible importance of their deregulation for expression in malignant lesions are discussed.

Transforming growth factor beta1 induces differentiation in human papillomavirus-positive keratinocytes.

Human papillomaviruses (HPVs) are implicated in the etiology of anogenital cancers. Expression of the HPV E6 and E7 oncoproteins is believed to contribute to the carcinogenic process. Progressive loss of the ability to differentiate and resistance to the growth-inhibitory effects of endogenous signals also appear important in multistep tumorigenesis. Transforming growth factor beta1 (TGF-beta1) is a potent growth inhibitor for a variety of cultured cells. There have been conflicting reports on the ability of TGF-beta1 to inhibit the growth of HPV-positive keratinocytes in monolayer cultures. We have employed the organotypic (raft) tissue culture system, which more accurately mimics the in vivo cellular environment and architecture. We have investigated the TGF-beta1 response of HPV-positive keratinocytes derived from neoplastic cervical biopsies. Growth of these cell lines as raft tissues showed that many were altered in the ability to stratify and synthesize differentiation-specific proteins. When the organotypic tissues were treated with TGF-beta1, a more complete differentiation of the keratinocytes was induced. Treatment with 12-0-tetradecanoylphorbol-13-acetate gave similar results. TGF-beta1 treatment of HPV-positive raft epithelia led to a dose-dependent increase in E7 RNA expression in contrast to results from previous studies with monolayer cultures. Furthermore, TGF-beta1 interfered with the proliferation of HPV-positive cell lines grown in monolayer cultures. Our results suggest that loss of the ability to express markers of differentiation, a characteristic of malignancy, is a two-step process. The first step is reversible; the second is irreversible.

Splice sites of human papillomavirus type 16 E6 gene or heterologous gene required for transformation by E7 and accumulation of E7 RNA.

Transformation of primary baby rat kidney cells by the human papillomavirus type 16 (HPV 16) E7 gene and efficient accumulation of E7 RNA have been shown by this laboratory to depend on the integrity of the nucleotide position (nt) 880 splice donor site. Here, the splice sites within the HPV 16 E6 open reading frame (ORF) and the sites of the SV40 splicing unit were examined for an ability to provide this requirement. Constructs containing the HPV 16 E6 sites and the SV40 splice site sequences were used for transformation and RNase protection assays. E6 splice sites supported a low level of transformation, in assays for complete HPV 16 early region constructs containing loss-of-function mutations of the nt 880 site. Using constructs with wild-type E6 or SV40 splice sites showed that both splice sites could substitute similarly for the requirement in cis of the nt 880 site for transformation. HPV 16 E6 mutated splice site and SV40 splice site in reverse, nonfunctional orientation relative to the promoter, were not transformation competent. The HPV 16 E7 RNA levels for the E6 splice site constructs correlated closely with the transformation frequency. The SV40 splice sites were required for E7 transcript accumulation. The results showed E6 splice site function and evidence for enhanced exon skipping from E6 splice donor site to acceptor sites 3' of the E7 ORF. This was shown with constructs containing loss-of-function mutations of the nt 880 site. These results confirmed the function of the splice sites by the transformation competent constructs and suggested lower transformation frequency than for wild type was due to skipping of the E7 exon. These patterns of transcripts may have a role in the regulation of gene expression during progression to malignancy. The combined results revealed that the general presence of a functional splice donor site was absolutely required for transformation by HPV 16 E7 and accumulation of E7 RNA.

Noncoordinated responses of branched-chain alpha-ketoacid dehydrogenase subunit genes to dietary protein.

The response of the murine genes encoding the subunits of branched-chain alpha-ketoacid dehydrogenase complex (BCKAD) to changes in dietary protein was determined. Steady-state RNA levels for two of the subunits, E1 beta and E2, decreased by two- to four-fold in the livers of mice fed 0% protein isocaloric diets compared to the levels observed in mice fed standard (23%) or high (50%) protein isocaloric diets. In contrast, the levels of RNA encoding the E1 alpha subunit did not change significantly in response to these dietary protein changes. The hepatic decreases in E1 beta and E2 RNA associated with 0% protein isocaloric diets were reversible, with prompt return to baseline levels following 48 hours of 50% protein isocaloric diets ad libitum. In kidney, no significant changes in the RNAs encoding any of the three BCKAD subunits were observed in response to changes in dietary protein. Studies of RNA variations associated with growth and development in several murine tissues, including liver and kidney, demonstrated coordinated changes between all subunits. Similar coordinated changes were observed during 3T3-L1 adipocyte differentiation. These studies suggest that the responses of the BCKAD subunit genes to alterations in dietary protein are noncoordinated and tissue-specific, in contrast to the coordinated changes observed during growth and/or differentiation. The differences in BCKAD subunit RNA levels observed under varying nutritional and developmental conditions suggest that multiple regulatory mechanisms modulate BCKAD subunit expression.

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA.

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA.

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

In vitro cleavage of HPV16 E6 and E7 RNA fragments by synthetic ribozymes and transcribed ribozymes from RNA-trimming plasmids

A RNA-trimming plasmid pRG523 is constructed, in which three Rz genes, GR5(5'- cis-Rz gene), HR2G( trans-Rz gene) and GR3(3'- cis-Rz gene), are arranged in the order from 5' to 3' downstream from the T7 promoter. In vitro transcription of this plasmid shows that the trans-Rz can be trimmed to definite lengths by the cis-Rz on both sides of the trans-Rz. In vitro cleavage of HPV16 E6 and E7 RNA fragments of different lengths by synthetic Rz and that of E7 RNA with a length of 171 nt by synthetic Rz and transcribed Rzs with different lengths of flanking sequences is studied. The results show that the non-base-pairing flanking sequences on both Rz and target RNA can affect the cleavage reaction.

Cleavage of Cottontail Rabbit Papillomavirus E7 RNA with an anti-E7 Ribozyme

We have designed and constructed a plasmid (pE7RZ-1) that contains a gene for a hammerhead ribozyme that specifically cleaves cottontail rabbit papillomavirus (CRPV) E7 RNA sequences in vitro. The in vitro produced transcripts of pE7RZ-1 cleave CRPV E7 target sequences in trans at 37°C. Pretreatment of pE7RZ-1 RNA with poly-L-lysine (PLL) increases the stability of the RNA to greater than 2 hours in the presence of a crude papilloma cell extract and the pE7RZ-1 RNA/PLL mixture retains catalytic activity in this system. This is the first report of a papillomavirus specific ribozyme RNA cleavage and leads the way for the design of effective papillomavirus specific ribozyme based therapies.

Glucocorticoid-dependent transformation by human papillomavirus type 16 E7 coding and 3′ noncoding sequences

The establishment of transformation of primary rodent cells by human papillomavirus (HPV) type 16 DNA requires glucocorticoid hormones (Pater et al., Nature 335, 832–835, 1988). Here we provide evidence by mutational analysis that, in the context of the hormone-regulated HPV 16 prom oterlenhancer, the only protein coding sequences of HPV 16 required are those of the E7 gene. Moreover, additional sequences adjacent to the 3' end of E7 coding sequences are also essential for the establishment of the transformed phenotype. Splice donor sites, especially an E7 ORF 3′ proximal one, are implicated for this cis-acting function, since specific deletion mutations of these splice sites greatly or completely reduced the frequency of transformation and the level of E7 RNA.

Nucleotide 880 splice donor site required for efficient transformation and RNA accumulation by human papillomavirus type 16 E7 gene.

Mutations within coding sequences of the various human papillomavirus type 16 (HPV-16) genes have been used to demonstrate that the HPV-16 E7 gene is necessary and sufficient for transformation of rodent cells. We now provide evidence that, in addition to E7 coding sequences, a small cis-acting region immediately flanking the 3' end of E7 coding sequences is also required for transformation. This was shown by translation termination linker insertion, progressive deletion analysis, and site-directed mutagenesis. Disruption of the nucleotide (nt) 880 splice donor site within the 3'-flanking region by deletion of as few as 4 nt or substitution of 3 nt totally abolished transformation. Regeneration of the wild-type sequence in a previously transformation-incompetent splice site mutant restored transformation. Mutating the wild-type splice donor site to the consensus splice site resulted in a stronger transformation phenotype, while mutating the +2 position of the consensus sequence significantly reduced the frequency of transformation. It was shown with RNase protection assays that the amount of E7 mRNA in transformation-deficient splice site mutants was much lower. Nuclear runoff experiments revealed that there was no change in the rate of synthesis of E7 message in the nt 880 splice site mutant. Furthermore, mutations of HPV-16 sequences indicated that the two other early region splice donor sites have no more than minor roles in transformation and efficient RNA accumulation. These results indicate that the specific integrity of the nt 880 splice donor site is essential for both accumulation of E7 RNA and efficient E7-mediated transformation.

Transforming growth factors beta 1 and 2 transcriptionally regulate human papillomavirus (HPV) type 16 early gene expression in HPV-immortalized human genital epithelial cells

Human papillomavirus type 16 (HPV16) early proteins E6 and E7 have been implicated in maintenance of the malignant phenotype in cervical cancer. Transforming growth factors beta one and two (TGF betas 1 and 2), polypeptides that regulate cellular growth and differentiation, reversibly inhibited expression of the HPV16 E6 and E7 genes in several immortal genital epithelial cell lines. Loss of E6 and E7 protein expression followed a dramatic time- and dose-dependent decrease in E6 and E7 RNA levels and was accompanied by cessation of cell proliferation. TGF betas 1 and 2 inhibited HPV16 RNA expression at the transcriptional level; inhibition was dependent upon ongoing protein synthesis. TGF betas 1 and 2 also induced a six- to sevenfold increase in TGF beta 1 RNA. Cells became partially resistant to the inhibitory effects of TGF beta 1 on cell growth and HPV early gene expression after prolonged cultivation in vitro or after malignant transformation. Thus, TGF beta 1 may function as an autocrine regulator of HPV gene expression in infected genital epithelial cells.

The adenovirus E4 gene, in addition to the E1A gene, is important for trans-activation of E2 transcription and for E2F activation

Previous experiments have demonstrated that adenovirus infection of human and mouse cells leads to an E1A-dependent activation of the DNA-binding capacity of a cellular transcription factor termed E2F. E2F binds to two sites in the adenovirus E2 early promoter which have been shown to be critical for E1A-dependent E2 early transcription, and the E2F-binding sites can confer E1A-induced transcription to a heterologous promoter. In addition, under a variety of circumstances, the increase in E2F-binding activity coincides with the activation of E2 transcription. We now find that, in addition to the E1A gene, another early viral gene, the E4 gene, is necessary for the activation of E2F-binding activity. Extracts prepared from human 293 cells, which express the E1A and E1B genes, had low levels of E2F activity, whereas infection of 293 cells with the E1A mutant dl312 increased E2F activity. This increase did not occur when 293 cells were infected with dl366, an E4 deletion mutant, nor was there an increase in E2F activity in HeLa cells infected with either dl366 or dl312; however, a coinfection with the two mutants yielded the normal wild-type increase in E2F. Furthermore, infection of HeLa cells with a high multiplicity of dl312, conditions that allow E4 gene expression in the absence of E1A, did not yield an increase in E2F activity. Thus, it appears that both the E1A gene and the E4 gene are directly involved in E2F activation. Measurements of E2 RNA production in a dl366 infection as compared with a wild-type or dl312 infection demonstrate that the E4 gene is essential for full E2 transcription. Furthermore, transfection assays of the E2 promoter demonstrate that, although E1A alone can trans-activate the E2 promoter, it is not as effective as the combination of E1A and E4 in the induction of the E2 promoter. We therefore conclude that the activation of the E2F factor leading to the activation of E2 transcription requires the combined action of both the E1A 289-amino-acid protein and an E4 product.

Patterns of region-specific chorion gene expression in the silkmoth and identification of shared 5′ flanking genomic elements

Time-dependent and cell-specific changes in concentrations of total RNA, of poly A+ RNA, and of specific mRNAs have been measured throughout silkmoth choriogenesis. Levels of total RNA and of poly A+ RNA are maintained throughout much of choriogenesis, but decrease at least fourfold during the very late period, in parallel with a decrease in overall protein synthesis. Very late period changes in total RNA and in poly A+ RNA are less pronounced in the aeropyle crown region, where a subset of chorion proteins is preferentially synthesized, than in the flat region. Maximal accumulation of the E1 and E2 chorion mRNAs occurs preferentially in the aeropyle crown region during the very late period. Uridine pulse-labeling studies suggest that E1 and E2 transcription is similarly aeropyle crown region-specific and immediately precedes the time of maximal E1 and E2 RNA accumulation and protein synthesis. Sequences from the 5′ flanking regions of E1 and E2 genes have been compared. Several oligonucleotide sequences are present in both genes, and some are duplicated. These are potential cis-acting, regulatory elements.

Accurate and efficient in vitro splicing of purified precursor RNAs specified by early region 2 of the adenovirus 2 genome.

Polyadenylated and deproteinized nuclear RNA precursors encoded by early region 2 of the adenovirus 2 genome are spliced in vitro by nuclear extracts prepared from MOPC-315 mouse myeloma cells. The in vitro reaction excises sequences from two introns and attaches 5' sequences to the mRNA body. The nucleotide sequence across the splice junctions in the E2 RNAs processed in vitro was investigated by performing primer extensions in the presence of dideoxynucleotides and direct sequencing on polyacrylamide gels. We conclude that the in vitro splicing reaction is accurate and has the same precision as that of in vivo E2 cytoplasmic mRNA prepared from Ad2 infected cells. The efficiency of in vitro splicing by the nuclear extracts is very high. Approximately 80% of E2 RNA precursor, on a molar basis, are spliced in vitro to a mature RNA. These findings provide evidence that a nuclear extract prepared from MOPC-315 mouse myeloma cells is capable of accurate and efficient splicing of E2 RNA precursors.