The 5'-terminal sequences of immunoglobulin messenger RNAs of a mouse myeloma

Increased half-life of mu immunoglobulin mRNA during mouse B cell development increases its abundancy

When B cells encounter antigen, the cells mature into terminally differentiated plasma cells and the amount of steady-state immunoglobulin (Ig) mu mRNA is increased 23-60-fold over the amount seen in earlier B cell stages. Most of this dramatic increase in Ig gene mRNA accumulation could be due to post-transcriptional regulation. We have treated a series of mouse cell lines fixed at different stages of B cell differentiation with an adenosine nucleotide analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) which specifically blocks synthesis of new RNA polymerase II transcripts. The amount of mu heavy chain cytoplasmic RNA, measured by quantitative Northern blot analysis at various times post DRB treatment, is reflective of the transcript's stability. The mu mRNA half-life values observed from the earliest-stage lymphomas (70Z/3 and WEHI-231) are about 1.9-4 hr, whereas the t1/2 of mu mRNA in the hybridomas (Hyb54.3C2 and IdG11) is about 13-17 hr. There is, therefore, a nine-fold maximal increase in half-life of the mu mRNA in the Hyb54.3C2 over that observed in the earliest stage (70Z/3) cells.

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.

Regulated production of mu m and mu s mRNA requires linkage of the poly(A) addition sites and is dependent on the length of the mu s-mu m intron

mRNAs encoding the membrane-associated (mu m) and secreted (mu s) forms of mu heavy chain are derived from transcripts of the same immunoglobulin gene by differential RNA processing. To help elucidate the mechanism that regulates the production of these two mu mRNAs during the course of B-lymphoid maturation, we produced a series of specifically modified mu-chain genes and studied their expression when transfected into cells representing either early or late developmental stages. We have established that proper regulation depends on linkage of the mu s and mu m poly(A) addition sites and the length of the mu s-mu m intron. Deletion of an 800 to 900-nucleotide segment from the central region of this intron abolishes regulation; replacement of this segment with miscellaneous DNA sequences restores it. From these results we propose a model in which regulation is principally achieved by competition between cleavage/polyadenylylation of the mu s site and splicing of the C mu 4 and mu m exons.

Tandem kappa immunoglobulin promoters are equally active in the presence of the kappa enhancer: implications for models of enhancer function

Transcription of immunoglobulin kappa genes is regulated by enhancer and promoter elements, both of which function in a tissue-specific fashion. We have studied the interaction of these elements by transfecting plasmacytoma cells with genes that have tandem kappa promoters located next to a single kappa enhancer and assaying these genes for transient or stable transcription. We find that the promoters located proximal and distal to the enhancer function identically whether they are separated by 440 bp or by 2.7 kb or whether they are located 1.7 or 7.7 kb away from the enhancer. Our results indicate that the immunoglobulin kappa enhancer does not operate as a bidirectional entry site for RNA polymerase or for other factors associated with the transcription complex. Rather, they suggest that the enhancer exerts its influence uniformly over large distances and independently of the presence of intervening promoters.

P31, a mammalian housekeeping protein encoded by a multigene family containing a high proportion of pseudogenes

The primary structure of P31, a 13.300 kDa mammalian 'housekeeping' protein, was deduced from the nucleotide sequence of a rat recombinant cDNA clone. The P31 mRNA has 950 nucleotides and codes for a protein of 121 amino acids. This mRNA is present in several mouse tissues and in other mammals. Nuclei of rapidly growing cells contain mature P31 mRNA and a distinctive set of larger transcripts. P31 is encoded by a multigene family. Five members of the family were isolated from a mouse genomic library and restriction mapping and S1 nuclease analysis of four of them (P31-4, P31-12, P31-13 and P31-14) suggest that they are processed genes. The very low homology of the fifth (P31-8) with respect to the corresponding cDNA sequence indicates that it is a pseudogene. Although the features of the mRNA and the genes encoding P31 exhibit extensive similarity with those of ribosomal proteins, neither the identity nor the biological function of the protein has yet been determined.

Nucleotide sequence of the satellite of peanut stunt virus reveals structural homologies with viroids and certain nuclear and mitochondrial introns

Peanut stunt virus-associated RNA 5 (PARNA 5), the satellite of a plant cucumovirus, is a linear RNA of 393 nucleotides with a 5' cap and a 3' hydroxyl group. Determination of its nucleotide sequence has revealed two consecutive open reading frames that together extend most of its length. Sequences at the 5' and 3' ends are homologous with those of the satellite of the related cucumber mosaic virus, and the double-stranded forms of both satellites contain an unpaired guanosine at the 3' end of the minus strand. However, little other homology exists between the two satellites. In contrast, PARNA 5 has several regions of 90% sequence homology with various plant viroids, including sequences of the conserved central region of most viroids. Such homologies suggest a common origin with viroids coupled with specific adaptation as a linear RNA. The presence within PARNA 5 of conserved intron sequences essential to proper RNA processing suggests a possible origin from plant introns and/or involvement of such sequences in the processing of PARNA 5 multimers to monomers at some stage of replication.

Nucleotide sequence of nuclear 5.4 S RNA of mouse cells

The nucleotide sequence of nuclear 5.4 S RNA, a new species of small nuclear RNA (snRNA) of mouse cells, was determined. The 5.4 S RNA consists of 138 nucleotide residues containing 1 mol each of 2,2,7- trimethylguanosine (m3(2,2,7) G), 2'-O-methyladenosine (Am), 2'-O-methyluridine (Um) and pseudouridine as modified nucleosides. This RNA has a cap structure, m3(2,2,7) ++GpppAm -, at its 5'-terminus and sequences complementary to the terminal consensus sequences of introns. The sequence complementary to the 5'-splice junction, A-U-C-C-psi-U-A-C-C-U-G, is very similar to the 5'-terminal sequence of U1 RNA.

Nuclear ligation of RNA polynucleotide kinase products

RNA polynucleotide kinase has been shown to transfer [gamma 32P] from ATP to 5-OH termini of endogenous nuclear RNA. The products of this reaction have been isolated in RNA larger than 125 after in vitro incubation of mouse L cell nuclei. About 20%-30% of these 5'-OH kinase products are polyadenylated. A sizeable fraction of the [gamma 32P] label from ATP is also found in internal phosphodiester bonds after 30-minute nuclear incubation in vitro. The possibility of substantial [32P] 1) 2mM nucleoside triphosphates in the incubation medium, 2) limited nearest-neighbor distribution 3' and 5' to the phosphodiester bond compared with that from [alpha 32P] UTP, 3) different nearest-neighbor distribution for RNA molecules greater than 125 and 12-3S, 4) relative insensitivity of the [gamma 32P] incorporation to alpha-amanitin as compared with total RNA synthesis, 5) internal [32P] appearance in RNA greater than 12S in less than five minutes of incubation, and 6) less than 0.03% to 0.6% of the total [32P] in the alpha position of nucleoside triphosphates after 30 minutes of incubation. The [gamma 32P] incorporation was dependent on high ATP concentration and was insensitive to competition by inorganic phosphate. These results are consistent with the levels of 5' RNA polynucleotide kinase activity in L cell nuclei and suggest the presence of an RNA ligase that can utilize the termini generated by the 5'-OH RNA kinase in a ligation reaction.

Functional significance and evolutionary development of the 5'-terminal regions of immunoglobulin variable-region genes

The 5'-terminal sequence of the kappa light-chain gene expressed in MPC11 plasmacytoma cells was definitively determined by analysis of both the kappa mRNA and the gene from which it is transcribed. The distance between the cap site and the translation initiation codon is only 3 nucleotides, and in a minor variant only 2 nucleotides, considerably less than that found in other species of nucleus-derived mRNA. S1 nuclease protection experiments with MPC11 nuclear RNA indicate that the cap sites are coincident with the transcriptional start sites, suggesting that the 5'-terminal heterogeneity is caused by imprecision in transcriptional initiation. A comparison of the 5'-terminal structure of the MPC11 V kappa gene with that of several other V genes indicates that the length of the first exon, which is composed of the 5' untranslated region which is composed of the 5' untranslated region and a sequence encoding most of the signal peptide, is highly conserved. Within this set of examples, the 5' untranslated region varies from 3 to 33 nucleotides, and the signal-peptide-coding block from 46 to 76 nucleotides. This analysis has also provided insight into the genetic origins for two anomalous properties of the MPC11 light chain.

On immunoglobulin heavy chain gene switching: two gamma 2b genes are rearranged via switch sequences in MPC-11 cells but only one is expressed

During B lymphocytes differentiation, switches in the expression of heavy chain immunoglobulin constant region (CH) genes occur by a novel DNA recombination mechanism. We have investigated the requirements of the CH gene switch by characterizing two rearranged gamma 2b genes from a gamma 2b producing mouse myeloma (MPC-11). One of the two gamma 2b genes is present in 2-3 copies per cell (gamma 2b strong hybridizer) while the other is present in approximately 1 copy per cell (gamma 2b weak hybridizer). Genomic clones of the gamma 2b strongly hybridizing gene indicate that this is an abortive switch event between the S gamma 3 and S gamma 2b regions. However, clones of the gamma 2b weakly hybridizing gene suggest a functional rearrangement due to the presence of VH, JH and S mu sequences. The switch-recombination sites of these rearranged gamma 2b genes and those of other CH genes show a high degree of preference for the sequence AGGTTG 5' of either the S mu donor site or the appropriate CH S acceptor site. AGGTTG and its analogs are rare in the S mu region, are somewhat prevalent in s alpha and in the case of S mu are found 5' of a tandemly repeated DNA sequence (GAGCT, GGGGT) comprising most of S mu.

Mouse beta-globin and adenovirus-2 major late transcripts are initiated at the cap site in vitro

Initiation of transcription on major late DNA of adenovirus serotype 2 and the beta-globin gene of the mouse was studied by using ribonucleoside [beta-32P]triphosphates as labeled precursors in vitro. The 5' termini of discrete runoff transcripts of both templates were preferentially labeled. The beta phosphate of the cap structure was labeled by [beta-32P]ATP but not [beta-32P]GTP, indicating that the beta phosphate of the cap is contributed by the initiating nucleoside triphosphate (ATP in both cases). Therefore, capping occurs on the initial nucleotide of these transcripts.

Activity of multiple light chain genes in murine myeloma cells producing a single, functional light chain

Two cloned lambda 1-producing myelomas (HOPC-1, MOPC-104E) contain rearranged kappa genes and levels of mature-sized kappa RNA comparable to those found in kappa-producing myeloma cells. Another lambda 1-producing myeloma tumor line (HOPC-2020) and a lambda 1-containing B cell leukemia line (BCL1) also contain significant levels of kappa RNA. One lambda 11-producing line (MOPC-315) contains no detectable kappa RNA, but it also has no kappa genes in the embryonic configuration. kappa-related proteins are not detectable in the lambda 1-producing lines by standard procedures, but by sensitive methods at least two lines contain kappa protein fragments. The MOPC-104E line produces both a 14.5K kappa fragment that is not readily detectable because of its low rate of synthesis and short half-life (T 1/2 less than 5 min), and a major 16.5K protein that lacks kappa cross reactivity but is demonstrable by translation of purified MOPC-104E kappa RNA. The HOPC-1 kappa RNA also encodes a short-lived 14K kappa fragment. The MPC-11 line, which produces a mature kappa RNA and protein as well as an 800 base kappa fragment RNA and kappa protein fragment, has both kappa alleles rearranged, one apparently aberrantly between J and C kappa. Two different kappa RNA species, one the same size as the MPC-11 kappa fragment RNA, frequently are present in kappa RNA-containing Abelson murine leukemia virus-transformed lymphoid cells as well as in 18 and 19 day murine fetal liver. For light chains, neither allelic nor isotype exclusion is generally evident in myeloma and lymphoma cells; rather both produce only a single functional light chain. Models of light chain activation must explain restriction by considering the functional properties of the light chain rather than light chain gene expression.

Tissue-specific expression of mouse-alpha-amylase genes: nucleotide sequence of isoenzyme mRNAs from pancreas and salivary gland

We have determined the nucleotide sequence of two different mouse alpha-amylase mRNAs, one found in the pancreas and the other in the salivary gland. The 1577 and 1659 nucleotide mRNAs from pancreas and salivary gland, respectively are the major alpha-amylase species which accumulate in each tissue. Differences in mRNA length are primarily in the 5' noncoding regions. Comparable portions of the mRNAs are 89% homologous. The mRNA sequences predict alpha-amylase precursor proteins of 508 and 511 amino acid residues, accounting for nearly the entire coding capacity of the mRNAs; differences in protein length occur as a result of a nine nucleotide segment present within the translated portion of salivary gland, but not pancreas, mRNA. The lengths and amino acid compositions of the predicted proteins concur with those determined empirically by others. These proteins differ 12% in amino acid sequence, explaining previously observed differences in net charge and antigenic properties. Finally, translation of the salivary gland alpha-amylase mRNA is not initiated at the AUG codon nearest the 5' terminus since that codon is almost immediately followed by the termination triplet UAA. This observation may have implications for the mechanism of translation initiation in eucaroytes.

The modified nucleotide constituents of human prostatic cancer cell (MA-160) poly(A)-containing RNA

Cytoplasmic poly A(+) RNA from human prostatic cancer cells grown in the presence of 32P was isolated by affinity chromatography on columns of oligo(dT)-cellulose. The RNA was digested with RNAase T2 and the products of digestion were fractionated by two-dimensional electrophoresis. The resulting autoradiograms revealed the presence of many different cap groups as well as two internal modified nucleotide components. 19 different type 1 and type 2 'cap' groups were identified. The internal modified nucleotides were N6-methyl adenosine and a 2'-O-methyl nucleotide possessing an unusual modified base.

Post-transcriptional modifications of oat coleoptile ribonucleic acids. 5'-Terminal capping and methylation of internal nucleosides in poly(A)-rich RNA

Evidence is presented for the occurrence of 5'-terminal capping structures in poly(A)-rich RNAs from oat coleoptile tissue. Similar to the cap structures in mRNA from other eukaryotic organisms, the 5' terminus of these oat coleoptile RNA molecules consists of 7-methylguanosine joined 5' to 5' with the adjacent (penultimate) nucleoside by means of three phosphate groups in two pyrophosphate linkages. The penultimate nucleoside contains primarily purine bases, but small amounts of pyrimidines (cytidine) are also detectable. Some monophosphorylated 5'-termini were also detected, however, they appear to occur as a result of RNA degradation. In addition to the 5 cap, oat RNA molecules are also post-transcriptionally modified with a low frequency of N6-methylations of internal adenosines.

Nuclear transcripts of mouse heavy chain immunoglobulin genes contain only the expressed class of C-region sequences

In plasmacytoma cells producing IgG, IgA, or IgM immunoglobulin heavy chains, the large precursors of the heavy chain messenger RNA's contain nucleotide sequences that specify only the expressed class of constant region. This indicates that the switch from one class of heavy chain to another during B cell ontogeny does not occur by altered processing of a complex gene transcript.

Selective suppression of the transcription of ribosomal genes in mouse-human hybrid cells

Mouse-human hybrid cells that preferentially segregate either mouse or human chromosomes were analyzed for their relative content of mouse and human rRNA genes and for their capacity to transcribe these genes. A distinctive Hind III restriction fragment containing 28S rRNA sequences was used to distinguish between mouse and human rDNA and a set of distinctive loop structures in the 45S pre-rRNA was used to distinguish between mouse and human gene transcripts. Our results indicate that the genes of only one species are transcriptionally active in these hybrid cells, even though both sets of genes are present.

Structural analysis of the fibroin gene at the 5' end and its surrounding regions

Using the genomic clones of the fibroin gene with its flanking sequences, a detailed restriction map was prepared with particular attention given to the region neighboring the 5' end of the gene. About 60% of the fibroin mRNA has a complete cap (m7GpppAmUmCXG), and the remaining 40% has an unmethylated cap (GpppAPyXXG). The latter can be radioactively labeled by the use of vaccinia capping enzymes. Using the labeled mRNA, we mapped the 5' end of the gene by hybridization to restriction enzyme digests. DNA sequencing of this region revealed a sequence ATCAGCATCAG that corresponds to ApyXXG in tandem. The 5' end of mRNA with a complete cap was also located in these 11 nucleotides. Since the second ATCAG region was protected from S1 digestion following hybridization with total fibroin mRNA, we have tentatively assigned it as the sole 5' end of the transcription unit. About 700 bp were sequenced in the region from -800 + 1700 bp. The region of about 210 bp preceding the 5' end of the gene which may accommodate a promoter sequence is very AT-rich and contains clusters of A and T residues. This region contains statistically significant dyad symmetries, direct repeats and inverted repeats. At -30 to -24, the sequence TATAAAA was observed, and this is similar to a Pribnow-type sequence (TATAGATG). The sequence that codes for the gly-ala repetitious peptide characteristic of fibroin begins somewhere between 1340 and 1600 bp from the 5' end. An intervening sequence of about 1.1 kb that interrupts the gene about 70 bp from the 5' end was detected by R loop formation. Structures of the fibroin gene cloned from fibroin producing and nonproducing cells look the same, especially around the 5' end and the intervening region.

Multiplicity of germline genes specifying a group of related mouse kappa chains with implications for the generation of immunoglobulin diversity

The number of germline genes specifying the variable sequences of the Vkappa21 group of light chains was determined by saturation hybridisation analysis to be four to six. This gene multiplicity is considerably less than the total variability in the group, indicating that kappa-chain diversity is generated by somatic mutations in both framework and complementarity-determining (hypervariable) regions.

The synthesis and processing of the messenger RNAs specifying heavy and light chain immunoglobulins in MPC-11 cells

The nuclear precursors of the immunoglobulin messenger RNAs of MPC-11 cells were characterized with respect to size, amount per cell and extent of polyadenylation. These cells produce three Ig mRNAs: a 1.8 kb component coding for a gamma2b heavy chain (H mRNA), a 1.2 kb mRNA coding for a k light chain (L mRNA) and a 0.8 kb mRNA coding for the constant region portion of the k light chain (Lf mRNA). To identify the pre-mRNAs without ambiguity, we constructed recombinant DNA plasmids containing H and L cDNA sequences, and used the cloned cDNAs as hybridization probes for analysis of steady state nuclear RNA and in DNA excess hybridization experiments with pulse-labeled nuclear RNA. The nuclear molecules containing Ig sequences consist of an 11 kb component (H1), which we believe to be the primary transcript of the H gene, 5.3 kb (L1), and 3.3 kb (L2) components, which seem to be primary transcripts of the L and L1 genes, components corresponding to mature size H, L and Lf mRNAs, and several intermediate-sized components which include the processing derivatives. The precursor role of these nuclear molecules was established by studies of their labeling kinetics and by appropriate pulse-chase experiments. All the pre-mRNA species including H1, L1 and L2 contain poly(A), thus suggesting that polyadenylation is an early event in the processing of these mRNAs. The MPC-11 cell contains about 30,000 and 40,000 cytoplasmic H and L mRNA molecules, respectively, which must be produced within one cell generation (approximately 24 hr). In comparison, the nucleus contains about 100-150 molecules of total pre-mRNA and only about 10-15 molecules of presumptive primary transcripts for each of these Ig species. These values indicate very rapid transcription rates (greater than 20 transcripts per min) and exceptionally fast processing rates (approximately 0.5 min for the primary transcripts and approximately 5 min for overall nuclear processing) for the Ig mRNAs. Thus rapid transcription and processing, together with high cytoplasmic stability, account for the high abundance of Ig mRNAs in the myeloma cell.