Determination of nucleotide sequences from double-stranded regions of HeLa cell nuclear RNA

Longer-than-unit-length viroid minus strands are present in RNA from infected plants

Nucleic acids isolated from uninfected and potato spindle tuber viroid-infected Rutgers tomato plants were fractionated on agarose gels under two different sets of denaturing conditions and hybridized to (125)I-labeled viroid in a series of blot hybridization experiments. Complementary strand nucleic acids detected in extracts of infected plants were heterogeneous in size, with four discrete bands containing molecules approximately 700, 1050, 1500, and 1800 nucleotides long. Enzymatic studies indicated that these viroid minus strands are composed exclusively of RNA and, as extracted, are present in complexes containing extensive double-stranded regions. After treatment with several RNases under conditions favoring digestion of single-stranded regions, the high molecular weight minus strands can no longer be detected and roughly unit-length minus strands appear. A model for the structure of the viroid replication intermediate is proposed.

RNA interference and mRNA silencing, 2004: how far will they reach?

The discoveries of RNA interference and RNA-mediated posttranscriptional gene silencing have opened an unanticipated new window on the regulation of gene expression as well as a facile and highly effective tool for knocking down gene expression in many organisms and cells. In addition, RNA interference and RNA silencing may conceivably be exploited for human therapeutics sometime in the future, possibly bringing greater clinical impact than have the so far disappointing antisense endeavors. This essay summarizes recent developments and offers some personalized perspectives, with emphasis on what we do not yet know.

The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element

A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse B1 sequences, and is represented as follows: direct repeat-CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition.

Direct analysis of the mini-exon donor RNA of Trypanosoma brucei: detection of a novel cap structure also present in messenger RNA

The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting and sequencing techniques, mini-exon oligonucleotides were identified and characterized. We detected a novel 5' terminal capped oligonucleotide present in both medRNA and mRNA. This structure contained m7G and at least four modified nucleotides, not identified previously. If the T. brucei mini-exon has exactly four transcribed nucleotides upstream from its originally designated 5' end, it would begin with the sequence: m7GpppA*A*C*U*AA*CG (asterisks denote modification) and medRNA would be 140 nucleotides long, excluding the m7G residue. The mini-exon contains, and retains during its transfer to mRNA, a novel 5' terminal structure whose presence could confer unique functional attributes.

Localization of Epstein-Barr virus-encoded small RNAs by in situ hybridization

Human B lymphocytes latently infected with Epstein-Barr virus (EBV) synthesize two low molecular weight RNAs designated EBER 1 and 2. Using an in situ hybridization technique we have localized EBER 1 and 2 within the nucleus of single EBV-harboring B lymphocytes from established and recently transformed cell lines. As controls, the locations of the small nuclear RNA, U1, and the small cytoplasmic RNA, 7SL, were examined in HeLa and EBV-harboring cells. Because of possible functional similarities between EBERs and the adenovirus-associated (VA) RNAs, VAI was also localized; it appeared to be in the nucleus and cytoplasm, implying that VAI may have a different role than that of the nuclear-localized EBERs.

Direct characterization of influenza viral NS1 mRNA and related sequences from infected HeLa cells and a cell-free transcription system

The NS1 mRNA of the influenza A virus WSN (H0N1) strain was isolated from a cell-free transcription system, and from the cytoplasm of virus-infected HeLa cells. The 32P-labeled NS1 mRNA derived from the infected cell cytoplasm was characterized by the secondary enzymatic analysis of sixteen of its large or distinct RNAase T1-resistant oligonucleotides. Several WSN strain-specific nucleotide differences from the previously-determined sequence of NS1 mRNA from the PR8 (H0N1) strain of influenza A virus, were located within these sequences. The RNAase T1-resistant oligonucleotides were placed within the primary sequence of NS1 mRNA, using the PR8 strain sequence data. The resulting linear map was then used to identify NS2 mRNA isolated from the infected cell cytoplasm, and an NS-related RNA species generated from NS1 mRNA incubated in a HeLa cell-free extract.

A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori

A library of low Cot DNA (Cot is the molar concentration of DNA times the incubation time in seconds) from Bombyx mori was used to isolate five independent clones of highly reiterated sequences from the genome of this organism. Sequence analysis revealed that all five clones belong to a single family of repetitive DNA elements, which we have named Bm1, and whose reiteration frequency is approximately 2.3 X 10(4) copies per haploid genome. Probing of a Bombyx genomic library (in lambda phage) with a Bm1 clone reveals that this repetitive sequence is dispersed throughout the genome. The pattern of interspersion was confirmed by Southern blot mapping of a large (270 X 10(3) base-pairs) domain of the chorion locus of Bombyx, where at least 13 independent regions were found to hybridize to Bm1. Four additional Bm1 elements have been sequenced from a 4.8 X 10(3) base-pair genomic fragment containing an early chorion gene. Two of these four elements are bounded by short (4 to 12 base-pairs) direct repeats. The nine Bm1 elements which have been sequenced are greater than 88% homologous to each other, and tend to fall in at least two size classes (253 base-pairs and 450 base-pairs). Seven of the nine Bm1 elements have a short 6 to 10 base-pair oligo(A) sequence at the 3' end. A sequence of about 29 base-pairs at the 3' end, including the oligo(A), shows 86% homology to the equivalent 3'-terminal domain of human Alu family repetitive elements. A 129 base-pair domain at the 5' end of Bm1 shows 66% homology to a Drosophila valine transfer RNA gene; thus the 5' end of Bm1 may contain the split internal RNA polymerase III promoter that is characteristic of most transcribed tRNA-like retroposons. Dot-blot analysis of Bombyx RNA shows that Bm1 DNA is indeed transcribed, and that the transcripts are well-represented in the total RNA of an ovarian-derived permanent cell line and posterior silk glands early in the fifth instar, but are less abundant in the RNA of pupae or silk glands late in the fifth instar.

Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA

The positions of intramolecular crosslinks induced by irradiation with ultraviolet light were mapped into potato spindle tuber viroid RNA and HeLa 5S rRNA. Crosslinking in each of these molecules occurred at a single major site, which was located by RNA fingerprinting and secondary analysis (and additional primer extension studies in the case of the viroid). Various lines of evidence suggest that these crosslinks identify a previously undescribed element of local tertiary structure common to these two widely divergent RNA molecules: (i) both crosslinks occur in an identical eight-base context, with the sequence 5' GGGAA 3' on one side and the sequence 5' UAC 3' on the other; (ii) both crosslinks connect bases that are not thought to be involved in conventional hydrogen bonding, within regions usually depicted as single-stranded loops flanked by short helical segments; and (iii) both crosslinks connect a purine and a pyrimidine residue, and both may generate the same G-U dimer. Furthermore, it is likely that the crosslinking site is of functional significance because it is located within the most highly conserved region of the viroid sequence and involves bases that are essentially invariant among eukaryotic 5S rRNA molecules.

Unusual properties of two branched RNA's with circular and linear components

Irradiation with ultraviolet light was used to create two nonlinear RNA molecules. Circular potato spindle tuber viroid (PSTV) RNA was crosslinked at a single site to generate a figure eight-shaped molecule; 5S rRNA from HeLa cells was transformed into an alpha-shaped molecule with a small circular element and two arms (1). Crosslinked RNA's could be separated from their untreated counterparts by electrophoresis in polyacrylamide gels containing urea. The gel mobility of crosslinked PSTV was not altered by boiling, treatment with E. coli RNase III or glyoxalation. However, mild nuclease digestion ("nicking") produced derivatives which migrated more slowly than the starting material in gels of certain polyacrylamide concentrations, but not in others. Limited nuclease digestion of crosslinked 5S rRNA did not generate any detectable products with reduced mobility in the gels tested. Thus, the ability of the "nicking assay" to reveal circular elements within nonlinear RNA's can vary depending upon the composition of the gel chosen for analysis and on the size of the circular element relative to the rest of the molecule.

Nature and origin of the RNA associated with simian virus 40 large tumor antigen

Simian virus 40 (SV40) large tumor (T) antigen isolated from mammalian cells undergoing lytic or transforming infection is associated with small RNA fragments ("T-antigen RNA") that are protected from nuclease digestion. The rather high complexity of the ribonuclease T1 fingerprints of T-antigen RNA suggested that it is mainly derived from cellular heterogeneous nuclear RNAs. In the present study, 5'-32P-labeled T-antigen RNA was hybridized to monkey, mouse, and human Alu and SV40 DNA, and the nucleotide sequence of 37 T1 oligonucleotides was determined. The results suggest that the bulk of T-antigen RNA is derived from noncoding, double-stranded, ordered regions of cellular heterogeneous nuclear RNAs that exhibit sequence homologies with interspersed repetitive elements of the cellular genome. The possible biological implications of these results are discussed.

Structure and distribution of Alu family sequences or their analogs within heterogeneous nuclear RNA of HeLa, KB, and L cells

We studied the distribution of repetitive sequence elements capable of forming double-stranded regions in nuclear RNA of HeLa, KB, and L cells. In human RNA populations, we called these regions duplex Alu family RNA (dAfRNA) because they represent transcripts of the highly reiterated family of DNA regions known as "Alu family DNA" (Rubin et al., Nature (London) 284:372-374, 1980). Although the dAfRNA populations of both human cell lines (HeLa and KB) have low sequence complexity, they represent 5% of the total heterogeneous nuclear RNA and have identical fingerprints; mouse L-cell dAf-like RNA (which has a similar complexity) represents only 2% of the total heterogeneous nuclear RNA and has an entirely different fingerprint. We utilized Escherichia coli RNase III as a highly specific reagent for the recognition of RNA:RNA duplex structure. This enzyme cleaves within the six characteristic RNase T1-resistant oligonucleotides of HeLa- and KB-cell dAfRNA (Robertson et al., J. Mol. Biol. 115:571-589, 1977). In addition, the size of heterogeneous nuclear RNA from all three cell types is reduced from greater than 32S to about 15S after RNase III treatment. We conclude that this size shift is a result of cleavage within dAfRNA regions and that such regions are present in most or all of the large RNA transcripts of these cells.

A replication cycle for viroids and other small infectious RNA's

Experimental data concerning viroid-specific nucleic acids accumulating in tomato plants establish, together with earlier studies, the major features of a replication cycle for viroid RNA in plant cells. Many features of this pathway, which involves multimeric strands of both polarities, may be shared by other small infectious RNA's including certain satellite RNA's and "virusoid" RNA's which replicate in conjunction with conventional plant viruses. The presence, in host plans, of an elaborate machinery for replicating these disease agents suggests a role for endogenous small RNA's in cellular development.

Structure and distribution of Alu family sequences or their analogs within heterogeneous nuclear RNA of HeLa, KB, and L cells

We studied the distribution of repetitive sequence elements capable of forming double-stranded regions in nuclear RNA of HeLa, KB, and L cells. In human RNA populations, we called these regions duplex Alu family RNA (dAfRNA) because they represent transcripts of the highly reiterated family of DNA regions known as "Alu family DNA" (Rubin et al., Nature (London) 284:372-374, 1980). Although the dAfRNA populations of both human cell lines (HeLa and KB) have low sequence complexity, they represent 5% of the total heterogeneous nuclear RNA and have identical fingerprints; mouse L-cell dAf-like RNA (which has a similar complexity) represents only 2% of the total heterogeneous nuclear RNA and has an entirely different fingerprint. We utilized Escherichia coli RNase III as a highly specific reagent for the recognition of RNA:RNA duplex structure. This enzyme cleaves within the six characteristic RNase T1-resistant oligonucleotides of HeLa- and KB-cell dAfRNA (Robertson et al., J. Mol. Biol. 115:571-589, 1977). In addition, the size of heterogeneous nuclear RNA from all three cell types is reduced from greater than 32S to about 15S after RNase III treatment. We conclude that this size shift is a result of cleavage within dAfRNA regions and that such regions are present in most or all of the large RNA transcripts of these cells.

Studies on transcription termination and splicing of the rRNA precursor in vivo in the presence of proflavine

In isolated nucleoli from Tetrahymena thermophila, low concentrations of the intercalating agent proflavine inhibit both transcription termination and splicing of the rRNA precursor. Proflavine also exerts an in vivo effect on the process of transcription termination under conditions, where the growth rate is only slightly reduced. Thus, approximately 40% of the rRNA precursor molecules, accumulated in nucleoli during 60 min of treatment with the drug, are longer than the normal 35S rRNA precursor. R-Loop mapping of these longer precursor molecules isolated after 30 and 60 min of incubation demonstrates that the RNA polymerases have a 50 fold lower elongation rate in the spacer region than in the coding region. Proflavine in the given concentration is found to have no significant effect on the splicing of properly terminated precursor molecules. In contrast, none of the longer non-terminated molecules are found to be spliced. These results indicate that proflavine primarily affects the process of transcription termination and that the splicing event is inhibited due to the improper termination of the precursor molecule.

On the complementarity of long repeated sequences in DNA to hnRNA

Long repeated sequences containing up to 18,000 base pairs were found in a human DNA fraction isolated with the nuclease S1-dioxane method. Hybridization studies showed that the long repeats contained a greater proportion of sequences complementary to hnRNA than short repeats. They also exhibited homology to the latter, as shown by cross-hybridization experiments.

Human beta-globin promoter and coding sequences transcribed by RNA polymerase III

We have investigated low abundance RNAs transcribed in vitro and in vivo from the human beta-globin gene. These RNAs contain globin mRNA sequences covalently linked to sequences transcribed from the 5' flanking region between -235 and the mRNA cap site (+1). Their synthesis in vitro is sensitive to high (100 micrograms/ml) levels of alpha-amanitin but not to low (2 micrograms/ml) levels, and one region of the DNA template bordering their 5' termini is similar to a small segment of Alu repetitive DNA and to the RNA polymerase III promoter consensus sequence. Therefore, these RNAs are transcribed by RNA polymerase III but extend into the mRNA-coding region that is usually transcribed by polymerase II. The polymerase III transcripts are polyadenylated and are probably spliced. Their presence in bone marrow cells and peripheral blood reticulocytes implies that they play some role in the erythroid cell.

Genomic organization of rat rDNA

A detailed restriction map was determined for a 10.9 KB region that contains the initiation site for 45S pre-rRNA and the first 1.7 KB of the 18S rRNA coding region. When the restriction pattern of the cloned rDNA was compared with that of total rat DNA, the rDNA regions of both Sprague-Dawley and BD-9 rats were identical to each other and to that of the cloned rDNA. However, both strains exhibit a major polymorphism consisting of an insertion of 0.9 KB of DNA in the nontranscribed spacer between 0.29 KB and 1.8 KB upstream from the 45S RNA initiation site. This region consists of tandem repeats approximately 130 base pairs in length. These repeats contain large poly T tracts and are similar in sequence to analogous elements 5' to the origin of mouse rRNA transcription. Regions containing highly repetitious DNA sequences were located at sites 2.8 KB and 4.3 KB upstream from the initiation site. The repetitive sequence at 2.8 KB from the initiation site anneal to a known Alu-equivalent type 2 sequence derived from the second intron of the rat growth hormone gene.

Discrete and heterogeneous high molecular weight RNAs complementary to a long dispersed repeat family (a possible transposon) of human DNA

Approximately 1% of heterogeneous nuclear RNA and approximately 0.035% of cytoplasmic RNA from a cultured line of human lymphoblastoid cells is complementary to a long dispersed repetitious sequence that comprises at least 6% of human DNA. The complementary nuclear RNA is both heterogeneously and discretely sized and is present in both poly(A)-terminated and non-poly(A)-terminated molecules. The complementary cytoplasmic RNA is mainly in discretely sized molecules ranging in size from approximately 600 to 8200 bases, some of which are most abundantly represented in poly(A)-terminated molecules, whereas others are most abundantly represented in non-poly(A)-terminated molecules. Few, if any, of the complementary cytoplasmic RNAs can be found associated with polyribosomes. The dispersed repeat sequence exhibits substantial restriction enzyme fragment length polymorphisms in human DNA and is also present in mouse DNA, although some regions of the human repeat appear to be more abundantly represented in mouse DNA than are other regions.

Heterogeneous nuclear RNA promotes synthesis of (2',5')oligoadenylate and is cleaved by the (2',5')oligoadenylate-activated endoribonuclease

Heterogeneous nuclear RNA contains double-stranded regions that are not found in mRNA and that may serve as recognition elements for processing enzymes. The double-stranded regions of heterogeneous nuclear RNA prepared from HeLa cells promoted the synthesis of (2',5')oligoadenylate [(2',5')oligo(A) or (2'5')An] when incubated with (2',5')An polymerase. This enzyme is present in elevated levels in interferon-treated cells, and labeled heterogeneous nuclear RNA incubated with extracts of these cells is preferentially cleaved, since mRNA included in the same incubations is not appreciably degraded. The cleavage of heterogenous nuclear RNA is caused by the synthesis of (2'5')An and by a "localized" activation of the (2',5')An-dependent endonuclease, since it was enhanced by ATP, the substrate of the (2',5')An polymerase, and inhibited by 2'-dATP and ethidium bromide. Both of these compounds suppress the synthesis of (2',5')An, the first by competitive inhibition and the latter by intercalating into double-stranded RNA. The possible role of double-stranded regions and of the (2',5')An polymerase-endonuclease system in the processing of heterogeneous nuclear RNA is discussed.

Cytological localization of inverted repeated DNA sequences in Vicia faba

Inverted repeated DNA sequences have been isolated from sheared Vicia faba DNA by hydroxylapatite column chromatography, treated with nuclease S1, tritiated by the nick translation method and hybridized in situ on squashes of Vicia faba root tips. Silver grains appear grouped in a rather limited portion of interphase nuclei and form a sort of band across them. The central regions of metaphase chromosomes are preferentially labeled, labeling being excluded from telomeres, centromeres and secondary constrictions. These results are briefly discussed in relation to those obtained in other species and the functional significance of inverted repeats.

The Alu family of dispersed repetitive sequences

A family of related sequences that includes approximately 500,000 members is the most prominent short dispersed repeat family in primate and rodent DNA's. The primate sequence is approximately 300 base pairs in length and is composed of two imperfectly repeated monomer units, whereas the rodent repeat consists of only a single monomer. Properties of this repeat sequence, its flanking sequences in chromosomal DNA, and RNA's transcribed from it suggest that it may be a mobile DNA element inserted at hundreds of thousands of different chromosomal locations.

Characterization of the major Epstein-Barr virus-specific RNA in Burkitt lymphoma-derived cells

Cytoplasmic RNA prepared from five lymphoid cell lines and a Burkitt lymphoma biopsy was radioactively labeled in vitro and hybridized to cloned EcoRI restriction endonuclease fragments of B95-8 Epstein-Barr virus DNA. The results confirmed that the most abundant cytoplasmic RNA species in such cells is specified by a small region of the genome defined by the EcoRI J fragment. Detailed mapping experiments precisely localized these transcripts within the sequence of the rightmost one-third of the EcoRI J fragment. DNA sequencing suggested that this region of the Epstein-Barr virus genome is unable to code for protein. The major early transcripts consisted of two non-polyadenylated RNA species, each about 170 nucleotides in length. They were both transcribed off the same strand of the DNA and showed significant sequence homology with each other. The coding sequences of the two small RNAs contained potential intragenic control regions for RNA polymerase III.

Heterogeneous nuclear RNA promotes synthesis of (2',5')oligoadenylate and is cleaved by the (2',5')oligoadenylate-activated endoribonuclease

Heterogeneous nuclear RNA contains double-stranded regions that are not found in mRNA and that may serve as recognition elements for processing enzymes. The double-stranded regions of heterogeneous nuclear RNA prepared from HeLa cells promoted the synthesis of (2',5')oligoadenylate [(2',5')oligo(A) or (2'5')An] when incubated with (2',5')An polymerase. This enzyme is present in elevated levels in interferon-treated cells, and labeled heterogeneous nuclear RNA incubated with extracts of these cells is preferentially cleaved, since mRNA included in the same incubations is not appreciably degraded. The cleavage of heterogenous nuclear RNA is caused by the synthesis of (2'5')An and by a "localized" activation of the (2',5')An-dependent endonuclease, since it was enhanced by ATP, the substrate of the (2',5')An polymerase, and inhibited by 2'-dATP and ethidium bromide. Both of these compounds suppress the synthesis of (2',5')An, the first by competitive inhibition and the latter by intercalating into double-stranded RNA. The possible role of double-stranded regions and of the (2',5')An polymerase-endonuclease system in the processing of heterogeneous nuclear RNA is discussed.

mRNA in human cells contains sequences complementary to the Alu family of repeated DNA

Approximately one-half of the polysomal poly(A)+RNA from CCRF-CEM human lymphoblastoid cells associates at low R0t (10 M.sec) [where R0 is the initial concentration of RNA (M) and t is time (sec)] to form branched complexes detectable by electron microscopy. The complexes typically involve 2-16 molecules associated over double-stranded regions 120 +/- 30 base pairs long. Formation of such complexes suggests that poly(A)+RNA contains repeated-sequence elements that are highly represented in the mRNA population. Hybridization of polysomal poly(A)+RNA with a recombinant human DNA plasmid, p lambda H15C, which is shown to contain at least three regions complementary to two different members of the Alu family of DNA repeat sequences, showed a total of five regions where R loops are formed. The hybridized regions comprising these groups are 260 +/- 180, 240 +/- 170, 150 +/- 70, 180 +/- 60, and 180 +/- 80 base pairs long. The relative frequencies of R loops formed at these different sites indicate that sequences in this recombinant DNA are represented in the mRNA population at different frequencies. The hybridizing sequence of the RNA molecules is located near one terminus in 13% of the R loops and internally in 53% of the R loops. Surprisingly, 35% of the R loops apparently involve RNA molecules hybridized over their entire length of only 200 +/- 110 base pairs.

The occurrence of families of repetitive sequences in a library of cloned cDNA from human lymphocytes

A library of cloned cDNAs representative of lymphocyte total poly(A)+ RNA was screened with total DNA probes at high clone density. 10% of the recombinants showed the presence of sequences which are repeated in the genome. Further analysis of six such isolated cDNA clones indicated that they contain different families of repetitive sequences with reiteration frequencies of between 150 and 45,000 copies per haploid genomes. Five of the six clones were found to contain single copy sequences as well as a repetitive sequence. cDNA clones containing repetitive sequences have been found to be derived from high, intermediate and low abundance classes of lymphocyte poly(A)+ RNA.

The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element

A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse B1 sequences, and is represented as follows: direct repeat-CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition.

The evolution of a family of short interspersed repeats in primate DNA

Human DNA contains 300 nucleotide interspersed repeated sequences which mostly belong to a single family of sequences called the Alu family. This work examines the evolution of this family of sequences in primates. Bonnet monkey (Macaque radiata) DNA contains a predominant family of 300 nucleotide repeats which has nearly the same restriction map as the human Alu family and which hybridizes to human Alu family repeats under Southern blotting conditions. Prosimian (Galago crassicaudatus pangeniesis) DNA also contains a prominent group of 300 nucleotide long repeated sequences which does not have the same restriction sites as the human Alu family but which does hybridize to the human Alu family under reduced stringency conditions.

Presence of a highly repetitive and widely dispersed DNA sequence in the human genome

A genomic DNA library consisting of human DNA fragments about 18 kilobases long cloned in a bacteriophage lambda vector was found to contain a specific repeated DNA segment. The repeated sequence is present in greater than 95% of the genomic library, and selected clones contain at least two copies of the sequence. Our experiments indicate that this highly repetitive sequence (approximately 400,000 copies per haploid genome) is widely distributed in the human genome and is represented in the cytoplasmic polysomal mRNA. This sequence is homologous to the 300-base-pair Alu repeat family, the predominant repeat sequence in man.

Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome

We have cloned and partially characterized 24 loci from the human genome which are complementary to U1, U2, or U3, the three major species of small nuclear RNA (snRNA) in HeLa cells. When compared to the known U1 (human) and U2 (rat) snRNA sequences, the DNA sequences we report here for the complementary regions from two of the clones, U1.11 and U2.7, reveal the presence of truncated and divergent gene copies. Furthermore, most if not all of the 24 cloned loci contain gene copies that are significantly divergent from the homologous HeLa snRNA species because DNA from every recombinant phage except U1.7 and U1.15 proved unable to form snRNA.DNA hybrids which protect full-length HeLa snRNA from ild digestion with ribonuclease T1. Hence, we refer to these loci as snRNA pseudogenes. In both clones U1.11 and U2.7, an element of the dominant middle repetitive DNA sequence family in the human genome, the Alu family, is located upstream from the snRNA pseudogene and in the same orientation. Alu elements in the same location and orientation relative to bona fide genes have previously been found in the human beta-globin gene cluster [Duncan, C. H., Biro, P. A., Choudary, P. V., Elder, J. T., Wang, R. C., Forget, G. B., deRiel, J. K. & Weissman, S. M. (1979) Proc. Natl. Acad. Sci. USA 76, 5095-5099]. We discuss the significance of these findings in relation to the nature of snRNA multigene families and other reported examples of pseudogenes.

A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene

An unusually long repeated DNA sequence was identified in cloned DNA, three kb 3' to the human beta-globin gene. Other members of this repeated sequence family were isolated from a human genomic DNA library and characterized by Southern blotting techniques, electron microscopy, and solution hybridization. The copy located next to the beta-globin gene was found to be 6.4 +/- 0.2 kb long and continuous over that length. This repeated sequence family comprises about 1% of the human genome and contains 3000-4800 copies of moderate sequence divergence which are interspersed with other less-highly repeated DNA. The 6.4 kb repeated unit does not appear to be composed of any smaller tandemly repeated subunits, nor is it expressed at a high level in bone marrow cell RNA.

An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome

Evidence is presented that a homogeneous cytoplasmic species known as 7S RNA is the only abundant RNA in uninfected HeLa cells which can form strong hybrids with the dominant family of middle repetitive DNA sequences in the human genome. These DNA sequences are known collectively as the Alu family, because most of them share a common Alu I restriction site. When purified 7S RNA was hybridized to three different genomic clones containing Alu family DNA sequences, a specific region (or regions) comprising at most half the RNA sequence was protected from mild digestion with T1 ribonuclease; moreover, the hybrids between 7S RNA and cloned Alu family DNA wer imperfect, since T1 RNAase was able to nick the protected 7S RNA sequences under conditions where a true RNA: DNA duplex would have been resistant. This suggests that 7S RNA is encoded either by a small subset of the 300,000 Alu family sequences in the human genome or by an entirely different family of genes. The sequence of 7S RNA has been highly conserved through recent evolution, and in both avian and murine cells the RNA is selectively incorporated into oncornavirus particles during productive infection. The cellular function of 7S RNA is unknown.

The 5' flanking region of human epsilon-globin gene

The structural analysis of the 2.0 kb region upstream from the epsilon-globin gene has been carried out. A genomic DNA map around the gene was worked out in some detail to ensure that the cloned DNA was representative of the actual chromosomal arrangement. Furthermore, a new technique was developed to precisely map a reiterated DNA sequence present 1.5 kb to the 5' side of the gene. The complete nucleotide sequence of the 2.0 kb 5' flanking region was then determined and overlapped with the gene. The sequence included the reiterated DNA sequence which is homologous to the so-called AluI family of repeats. Unusual stretches of sequence 50 nucleotides long, where A + T represent about 90% of the bases, are present at both the 5' and 3' sides of the repeat.

Structure and in vitro transcription of human globin genes

The alpha-like and beta-like subunits of human hemoglobin are encoded by a small family of genes that are differentially expressed during development. Through the use of molecular cloning procedures, each member of this gene family has been isolated and extensively characterized. Although the alpha-like and beta-like globin genes are located on different chromosomes, both sets of genes are arranged in closely linked clusters. In both clusters, each of the genes is transcribed from the same DNA strand, and the genes are arranged in the order of their expressions during development. Structural comparisons of immediately adjacent genes within each cluster have provided evidence for the occurrence of gene duplication and correction during evolution and have led to the discovery of pseudogenes, genes that have acquired numerous mutations that prevent their normal expression. Recently, in vivo and in vitro systems for studying the expression of cloned eukaryotic genes have been developed as a means of identifying DNA sequences that are necessary for normal gene function. This article describes the application of an in vitro transcription procedure to the study of human globin gene expression.

Integration in vivo into simian virus 40 DNA of a sequence that resembles a certain family of genomic interspersed repeated sequences

The isolation and characterization of a viable mutant of simian virus 40 (SV40) called "in1449" are described. the mutant DNA is found to have a 157-nucleotide-long insertion at map position 0.649 within the 5' untranslated sequence of the early region of SV40. The complete nucleotide sequence of the insert is presented. Sequence comparisons show that the insert is not of SV40 origin. The insert is presumably of monkey origin since in1449 was produced within monkey kidney cells. The sequence of the in1449 insert matches remarkably well with sequences of a certain predominant family of interspersed repeated sequences in human DNA (called the Alu family) and cloned members thereof. This high degree of sequence homology suggests that the in1449 insert is derived from a member of a family of interspersed repeated sequences in monkey DNA related to the human Alu family. The in1449 insert (and the Alu family members) contain certain oligonucleotide sequences that also are found conserved in the replication origins of papovaviruses and certain other oligonucleotides found in repetitive double-stranded regions of mammalian heterogeneous nuclear RNAs. Sequences around the two recombinant joints in in1449 exhibit a definite pattern of homology. An octanucleotide present in the SV40 part of the first recombinant joint is exactly repeated 15 nucleotides away within the insert; another octanucleotide present within the insert at the second joint is exactly repeated 21 nucleotides away in the viral DNA. The viral DNA sequences flanking the insert in in1449 also exhibit some homology.

Electron microscope study of duck globin mRNA precursor crosslinked in situ

Double-stranded RNA segments present in duck globin pre-mRNA were crosslinked in situ with aminomethyltrioxalen and UV light. The secondary structure of the crosslinked pre-mRNA was then studied by electron-microscopic analysis of pre-mRNA . cDNA hybrids. The data suggest that duck globin pre-mRNAs contain intervening sequences that are excised stepwise. Excision and subsequent ligation appears to occur on precursor molecules that are stabilized by base-paired regions.

Specific RNA-cleaving activities from HeLa cells

Subcellular fractionation of HeLa cells was carried out under gentle conditions to isolate enzymes that cleave RNA precursors in a specific manner. Four separate activities--cleavage of HeLa cell heterogeneous nuclear RNA, the HeLa cell 45S rRNA precursor, RNA . DNA hybrids (RNase H), and the Escherichia coli tRNATyr precursor (RNase P)--were revealed by these studies. The specificity and limited nature of these cleavages suggest that they are due to eukaryotic RNA-processing enzymes. The virtual absence of random nucleases from these enzymes was demonstrated by their inability to cleave the 8000-base early mRNA precursor of bacteriophage T7, E. coli 30S rRNA precursor, or HeLa cytoplasmic poly(A)-containing RNA.

Ubiquitous, interspersed repeated sequences in mammalian genomes

DNA base sequence comparisons demonstrate that the principal family of 300-nucleotide interspersed human DNA sequences, the repetitive double-strand regions of HeLa cell heterogeneous nuclear RNA, and specific RNA polymerase III in vitro transcripts of cloned human DNA sequences are all representatives of a closely related family of sequences. A segment of approximately 30 residues of these sequences is highly conserved in mammalian evolution because it is also present in the interspersed repeated DNA sequences of Chinese hamsters. Further DNA sequence comparisons demonstrate that a portion of this highly conserved segment of repetitive mamalian DNA sequence is similar to a sequence found within a low molecular weight RNA that hydrogen-bonds to poly(A)-terminated RNA molecules of Chinese hamsters and a sequence that forms half of a perfect inverted repeat near the origin of DNA replication in papovaviruses.

Evidence for the role of double-helical structures in the maturation of simian virus-40 messenger RNA

Simian Virus-40 infected BSC-1 cells were pretreated with glucosamine and briefly pulsed with [3H]-uridine. The labeling can be halted instantaneously by the addition of cold uridine and glucosamine. Under these pulse-chase conditions, the inhibitory effects of the intercalating agent proflavine on the processing of prelabeled nuclear RNA precursors were examined in vivo. Proflavine inhibits the cleavage of viral nuclear RNA precursors. However, turnover of the mature viral mRNAs in the cytoplasm is not inhibited. The effect of proflavine on processing is not a secondary consequence of its inhibition of protein synthesis. The data suggest that base-paired secondary structures in the primary transcripts are important processing signals in the generation of viral mRNA molecules.