The structural organization of nuclear pre-mRNA. II. Very long double-stranded structures in nuclear pre-mRNA

DNA sequences homologous to long double-stranded RNA. Transcription of intracisternal A-particle genes and major long repeat of the mouse genome

Long double-stranded RNA (dsRNA-A) (Kramerov, D.A., Ryskov, A.P. and Georgiev, G.P. (1977) Biochim. Biophys. Acta 475, 461-475) from Ehrlich ascites carcinoma cells was used for the search for mobile dispersed genes in the mouse genome. Two kinds of genomic sequences hybridizing to dsRNA-A were cloned. They were designated A1 and A2. The A1 sequence was identified as the gene for intracisternal A particles, while the A2 sequence was found to be the major long repetitive sequence of the mouse genome. Melted dsRNA-A hybridized equally well to both DNA strands of A1 and A2 sequences while total poly(A)+ RNA bound preferentially to one of them. Thus, a partially symmetrical transcription took place in the case of A1 and A2 elements. The analysis of transcripts of A1 elements in Ehrlich carcinoma cells revealed RNAs with sizes of 9.5 kb, 6.8 kb and 6.0 kb. In plasmocytoma MOPC 21 cells, instead of the 6.0 kb RNA, two other kinds of RNA with sizes 5.3 kb and 7.8 kb were found. These transcripts poorly coincided with the four known variants of intracisternal A-particle (IAP) genes. It seemed that at least some of the described RNAs were transcribed from some minor non-identified variants of IAP genes. The A2 transcripts were practically restricted to nuclei, their sizes being heterogeneous.

Transposon-like sequences in extrachromosomal circular DNA from mouse thymocytes

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes and cloned into the HindIII site of lambda vector Charon 7. Fifty-six recombinants from this spc DNA library were analyzed. R repeats, which were originally found near immunoglobulin genes, were enriched in spc DNA clones relative to their representation in the chromosome. In one clone, the R sequence was linked to Bam and MIF sequences and the contiguous arrangement was truncated from both ends. In another clone, composite Bam/R and R repeats existed as a pair in inverted repeat orientation. Truncation occurred from the 5' side without affecting the 3' ends. In both clones, short direct repeats flanked the repeated sequences. The possible role of R sequences in transposition and circular formation is discussed.

Mouse ubiquitous B2 repeat in polysomal and cytoplasmic poly(A)+RNAs: uniderectional orientation and 3'-end localization

A cDNA library in pBR322 was prepared with cytoplasmic poly(A)+RNA from mouse liver cells. From 1 to 1.5% of clones hybridized to either B1 or B2 ubiquitous repetitive sequences. Several clones hybridizing to a B2 repeat were partially sequenced. The full-length B2 sequence was found at the 3'-end of abundant 20S poly(A)+RNA (designated as B2+mRNAx) within the non-coding part of it. B2+mRNAx is concentrated in mouse liver polysomes and absent from cytoplasm of Ehrlich carcinoma cells. The B2 sequence seems to be located at the 3'-end of some other mRNAs as well. To determine the orientation of the B2 sequence in different RNAs, its two strands were labeled, electrophoretically separated, and used for hybridization with Northern blotts containing nuclear, cytoplasmic and polysomal RNAs. In nuclear RNA, the B2 sequence is present in both orientations; in polysomal and cytoplasmic poly(A)+RNAs, only one ("canonical") strand of it can be detected. Low molecular weight poly(A)+B2+RNA [1] also contains the same strand of the B2 element. The conclusion has been drawn that only one its strand can survive the processing. This strand contains promoter-like sequences and AATAAA blocks. The latter can be used in some cases by the cell as mRNA polyadenylation signals.

Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing

Mouse genome contains two major families of short interspersed repeats in more than 10(5) copies scattered throughout the whole genome. They are referred to as B1 and B2 sequences since they were first isolated from the genome library by means of a dsRNA-B probe /1/. In this work, two copies of the B2 family were sequenced and compared with the previously sequenced B1 repeat /2/. A B2 ubiquitous repeat is ca. 190 bp long. The members of the family deviate in 3-5% of nucleotides from the consensus sequence. B2 contains regions of homology to the RNA polymerase III split promoter and to 4.5S snRNA I. Both B1 and B2 contain regions which resemble junctions between exons and introns. In contrast to B1, B2 does not contain apparent homologies to papova viral replication origins and a human Alu sequence. One side of the B2 repeat is represented by a very AT-rich sequence (ca. 30 bp long) followed with an oligo (dA) stretch 10-15 nucleotides long. This region of the repeat is the most variable one. The whole unit is flanked with 15-16 bp direct repeats different in sequenced copies of B2. The same is true of some copies of the B1 family. The properties of B1 and B2 repeats suggest that they may represent a novel class of transposon-like elements in eukaryotic genome. A possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.

The sequences homologous to major interspersed repeats B1 and B2 of mouse genome are present in mRNA and small cytoplasmic poly(A) + RNA

Heavy nuclear RNA contains high amounts of transcripts from repetitive sequences B1 and B2. Cytoplasmic poly(A)+RNA and, particularly, polysomal poly(A)+RNA (mRNA) also include these sequences but in smaller amounts. The abundant 2 kb mRNA of mouse liver are found to have a B2 sequence. These sequences are also found in a new class of low-molecular-weight heterogeneous (200-400 nucleotide long) poly(A)+RNAs. These RNAs are located mostly in cytoplasm rather than in polysomes. The amount of small B2+ RNAs is noticeable larger than that of small B1+ RNAs. Tumour cells seem to contain more small B2 RNA than normal cells. The hybridization tests show that extended homology exists between the B1 sequence and 4.5S small nuclear RNA, which is predicted from comparison of their base sequences. Also, we have found homology between B1 and small cytoplasmic 7S RNA. Hybridization of B2 to sn or sc RNAs has not been observed, although the sequencing reveals partial homology between B2 and 4.5S sn RNAI /1/.

Mobile dispersed genetic elements and their possible relation to carcinogenesis

In this paper, a hypothesis is described according to which mobile dispersed genetic elements are related to endogenous viral genomes and may be involved in oncogenic transformation by uptaking cellular genes important for cellular growth. It is also possible that, in certain cases, they can switch off the genes involved in the control of differentiation.

Double-stranded sequences in RNA of Drosophila melanogaster: relation to mobile dispersed genes

Double-stranded RNA (dsRNA) sequences were isolated from either total RNA or cytoplasmic poly(A)+RNA of D. melanogaster culture cells using a method described previously /1,2/. Virtually all dsRNA was found to be of high molecular weight (> 200 base pairs) and unable to snap back after RNA melting. Thus, it corresponds to one of dsRNA classes found in mouse cells, namely, to dsRNA-A /3/. Three different cloned DNA fragments of D melanogaster which hybridized to melted dsRNa were selected among 100 randomly taken. All of them efficiently bound poly(A)+RNA and high percentage of total cellular DNA. According to these and other properties, they were assigned to a group of mobile dispersed genes of D. melanogaster. DsRNA hybridizes to all subfragments of the two mobile dispersed genes tested (mdg 1 and mdg 3). Thus, complete transcripts of mobile dispersed genes are present in dsRNA. In total RNA, transcripts from one strand are more abundant than those from another one. DsRNA is heavily enriched in the transcripts from mobile dispersed genes as compared to total or poly(A)+RNA of the cytoplasm. It has been suggested that dsRNA in D. melanogaster is formed as the result of symmetric transcription of mobile dispersed genes. At least in the cytoplasmic fraction, two complementary strands are separated in vivo and may combine during the isolation of RNA.

The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA

Three copies of a highly repetitive DNA sequence B1 which is complementary to the most abundant class of mouse fold-back RNA have been cloned in pBR322 plasmid and sequenced by the method of Maxam and Gilbert. All the three have a length of about 130 base pairs and are very similar in their base sequence. The deviation from the average sequence is equal to 4% and the overall mismatch between each two is not higher than 8%. One of the recombinant clones used contained two copies of B1 oriented in the same direction. All of the B1 copies are flanked with sequences which possess nonidentical but very similar structure. They consist of a number of AmCn blocks (where m varies from 2 to 8 and n equals 1-2). These peculiar sequences in all cases are separated from B1 by non-homologous DNA stretches of 2-8 residues. In one case, a long polypurine stretch is located next to such a block. It consists of 74 residues most of which represent a reiteration of the basic sequence AAAAG. We have found two regions within the B1 sequence which are homologous to the intron-exon junctions, especially to those present in the large intron of the mouse beta-globin gene. It may indicate the involvement of the B1 sequence in pre-mRNA splicing.

Sequences hybridizing to mRNA, oligo(dT) and dsRNA from pre-mRNA are contiguous in the cloned mouse DNA fragments

Fragments from the DNA of mouse embryos produced by restriction endonucleases HindIII were cloned in pBR322 plasmid and examined for the ability to hybridize in situ with [32P] labeled cDNA synthesized from the polysomal poly(A)+mRNA template. Several of the selected clones were examined for the presence of specific sequences inside the cloned mouse DNA fragments by the blotting procedure of southern [1]. The data obtained indicate that the majority of the cloned mouse DNA fragments contained sequences hybridizing with cDNA, oligo(dT) and double-stranded regions from pre-mRNA. The results of hybridization experiments and double digestion with HindIII+HaeIII endonucleases provide evidence that these sequences could be contiguous in the given restriction DNA fragments.

Immunofluorescent detection of nuclear double-stranded RNA in situ in Vero and mosquito cells

Double-stranded RNA (dsRNA) was detected in situ by indirect immunofluorescence with antibodies to dsRNA. It was seen in nuclei of Vero and Aedes albopictus cells, but not in BHK cells, KB cells, chick embryo fibroblasts, or HeLa cells. Reactive dsRNA was present in the nucleoplasm, but not in nucleoli or cytoplasm. Extracted RNA from the whole cell contained from 0.08 percent (BHK) to 0.46 percent (HeLa) dsRNA, as estimated by serological methods. This dsRNA, found in molecules having the size distribution of heterogeneous nuclear RNA, did not renature rapidly after denaturation. The quantity of dsRNA in total extracted RNA did not correlate with the presence or absence of nuclear staining in situ.