Precursors of alpha and beta globin messenger RNAs

RNA processing of beta-globin transcripts containing 5' flanking and structural gene sequences

RNA species have been identified in murine erythroid cells which contain both 5' flanking and structural gene sequences from the beta maj globin gene. Two nonpolyadenylated RNA transcripts, average 3700 and 1800-1900 nucleotides long, were identified by denaturing agarose gel electrophoresis and were found to hybridize to both 5' and 3' beta maj globin flanking sequences. This finding suggests that transcription initiated in the 5' flanking region does proceed past the polyadenylation site. The apparent higher concentration of the 5' flanking sequences in precursor RNA molecules, as compared to mature polyadenylated globin mRNA, suggests increased precursor stability of beta globin transcripts initiated in the 5' flanking region.

Model for alternative RNA processing in human calcitonin gene expression

The alternative RNA processing pathways in human calcitonin gene (CALC-I gene) expression were investigated using steady state RNA isolated from human medullary thyroid carcinoma (MTC) and from a culture line derived from this tumor. On Northern blots the mature 1.0 kilobases (Kb) calcitonin (CT) - and 1.1 Kb calcitonin gene-related peptide (CGRP) mRNAs were detected with CALCI gene specific probes as well as high molecular weight poly (A) containing RNAs of 2.1, 2.3, 3.3, 4.2, 5.0 and 5.7 Kb. The 5.7 Kb RNA was identified as the poly(A) tailed primary transcript containing sequences corresponding to all 6 exons and 5 introns of the CALC-I gene. From the composition of the other RNAs the splicing order of the different introns could be deduced. The results suggest the following model. First all introns not involved in alternative processing (introns 1, 2 and 5) are spliced from the 5.7 Kb RNA in rapid successive reactions yielding a 3.3 Kb RNA, which accumulates. From this 3.3 Kb RNA, the last common intermediate in the alternative processing pathway, CT mRNA is formed by splicing of intron 3 and poly(A) addition at exon 4, in this order or the reverse order via 2.3 Kb or 2.1 Kb RNA intermediates respectively. Alternatively, the whole intron 3-exon 4-intron 4 region is spliced from the 3.3 Kb RNA yielding CGRP mRNA. The temporal sequence of poly(A) addition at exons 4 and 6 may relate to the observed structural differences between the poly(A) addition signals at these sites. The ratio of CT- to CGRP mRNA may relate also to the differences in the primary structures of the intron 3- and intron 4 splice acceptor sites.

Exon mutations that affect the choice of splice sites used in processing the SV40 late transcripts

The spliced species of late SV40 RNAs present in the cytoplasm of cells infected with various wild-type and mutant strains of SV40 that differ in their leader regions were determined using a novel modification of the primer extension method and the S1 nuclease mapping technique. These data indicated that mutations within the first exon of the late RNAs can affect dramatically the utilization of downstream donor and acceptor splice sites. In one instance, a ten base pair insertion within the predominant first exon increased utilization of an infrequently utilized donor splice site such that the small alteration became part of an intervening sequence, thereby suggesting a novel mechanism for regulation of gene expression. In addition, our method enabled detection of a previously unidentified spliced species, representing less than one percent of the SV40 late 19S RNA present in cells infected with wild-type virus, that may be an intermediate in the synthesis of a known doubly spliced 16S RNA species of SV40.

Messenger RNA turnover during bone marrow erythroid cell differentiation

Incubation of bone marrow cells from anaemic rabbits in the presence of actinomycin D led to a decrease in total protein synthesis and an increase in the relative synthesis of globin. This increase in the proportion of globin was observed with in vivo labelling of cellular proteins and in vitro translation of isolated RNA, which indicates that the messenger RNA for globin is much more stable than the other bone marrow cell messages. This was further shown by pulse-labelling the RNA and characterization of the different species by separation on a cDNA-oligo(dT)-cellulose column. Within 12 h after pulse-labelling the relative levels of globin mRNA had risen 10-fold, while a rapid decrease in the level of the poly(A)-rich RNA fraction was observed. Investigations into the mechanisms of this differential stability indicate that the more metabolically active cells from the early stages of erythropoietic development are more susceptible to inhibitors of RNA synthesis such as actinomycin D and alpha-amanitin. A preliminary study using a lysosomal inhibitor, chloroquine, indicates that there appear to be at least two degradative mechanisms, involving a lysosomal and a non-lysosomal pathway, with selective specificity for different messages.

Transcription unit of the rabbit beta 1 globin gene

We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

Transcription unit of the rabbit beta 1 globin gene

We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

High levels of intron-containing RNAs are associated with expression of the Drosophila DOPA decarboxylase gene

We have examined the structure and expression during embryonic development of the Drosophila DOPA decarboxylase gene, Ddc. The Ddc gene is transcribed to make at least five different size classes of RNA. These RNA species first appear late in embryogenesis, coincident with induction of Ddc enzyme activity. The most abundant and smallest RNA appears to be Ddc mRNA. The sequences encoding this RNA are split by two intervening sequences. Each of the larger RNA species contains some or all of the intervening sequences. We have noted two unusual features of Ddc expression during embryogenesis. First, the intervening-sequence-containing RNAs are present as 20% or more of the polyadenylated Ddc RNA molecules, an exceptionally high proportion. Second, these RNAs do not disappear as rapidly as Ddc mRNA after Ddc enzyme activity reaches fully induced levels. These observations indicate slow rates of RNA processing relative to mRNA half-life and suggest that post-transcriptional steps participate in regulating Ddc expression. Although four of the five RNA species were detected at multiple developmental stages during which Ddc is expressed, one was found uniquely during embryogenesis. This RNA differs from Ddc mRNA in length and in time of expression during embryogenesis but is transcribed in the same orientation and from the same genomic sequences as the Ddc primary transcript.

alpha-Amanitin-insensitive transcription of mouse beta major-globin 5'-flanking and structural gene sequences correlates with mRNA expression

A small proportion of the RNAs of mouse reticulocytes consists of beta major-globin mRNA sequences linked to sequences transcribed from the 5'-flanking region of the beta major-globin gene. These upstream RNAs are polyadenylylated and contain 700-800 nucleotides, and their 5' regions are heterogeneous. RNAs with similar or identical 5' regions are transcribed in cell-free extracts from a circular mouse beta major-globin gene template. Synthesis of most of the upstream RNAs in vitro is not inhibited by low levels (1 microgram/ml) of alpha-amanitin, indicating that they are transcribed by an enzyme(s) different from RNA polymerase II. During culture of mouse erythroleukemia cells with dimethyl sulfoxide, globin mRNA and upstream RNAs accumulate with similar kinetics. In contrast, upstream RNAs are not detected in hemin-treated cells.

High levels of intron-containing RNAs are associated with expression of the Drosophila DOPA decarboxylase gene

We have examined the structure and expression during embryonic development of the Drosophila DOPA decarboxylase gene, Ddc. The Ddc gene is transcribed to make at least five different size classes of RNA. These RNA species first appear late in embryogenesis, coincident with induction of Ddc enzyme activity. The most abundant and smallest RNA appears to be Ddc mRNA. The sequences encoding this RNA are split by two intervening sequences. Each of the larger RNA species contains some or all of the intervening sequences. We have noted two unusual features of Ddc expression during embryogenesis. First, the intervening-sequence-containing RNAs are present as 20% or more of the polyadenylated Ddc RNA molecules, an exceptionally high proportion. Second, these RNAs do not disappear as rapidly as Ddc mRNA after Ddc enzyme activity reaches fully induced levels. These observations indicate slow rates of RNA processing relative to mRNA half-life and suggest that post-transcriptional steps participate in regulating Ddc expression. Although four of the five RNA species were detected at multiple developmental stages during which Ddc is expressed, one was found uniquely during embryogenesis. This RNA differs from Ddc mRNA in length and in time of expression during embryogenesis but is transcribed in the same orientation and from the same genomic sequences as the Ddc primary transcript.

beta-Thalassemia in Chinese: use of in vivo RNA analysis and oligonucleotide hybridization in systematic characterization of molecular defects

To perform a systematic analysis of beta-thalassemia genes among Chinese, we have determined the DNA haplotype in the beta-globin gene region of 37 Chinese beta-thalassemia chromosomes. Only four haplotypes were found. Blot hybridization analysis of erythroid RNA from patients homozygous for haplotypes 1, 2, and 3 demonstrated different patterns, suggesting that a different mutation was associated with each haplotype. The mutation associated with haplotype 1 was a C----T substitution at IVS-2, position 654. This mutation produces a new donor splice site and leads to formation of a beta-globin RNA with an insertion of 73 nucleotides. The mutation associated with haplotype 2 was a nucleotide insertion of A between codons 71 and 72, which results in a frameshift and premature termination of beta-globin synthesis. Haplotype analysis suggests that these two mutations may account for up to 85% of beta-thalassemia genes in this ethnic group. The haplotype 3 gene contained a transcriptional "TATA" box mutation that has been previously reported. Oligonucleotide hybridization demonstrated that the mutation associated with haplotype 4 was the same IVS-1 position 5 substitution commonly observed among beta-thalassemia genes in Asian Indians. Since haplotype 4 of Chinese differs at polymorphic sites on either side of the IVS-1 position 5 mutation from the haplotype associated with this mutation in Indians, the mutation presumably arose independently in these two populations.

S1 mapping of purified nascent transcripts of simian virus 40

We purified nascent simian virus 40 late transcripts by incubating viral transcriptional complexes, isolated from infected BSC-1 cells, in a reaction mixture that contained mercurated CTP; RNA molecules that had incorporated mercurated residues in vitro were isolated by sulfhydrylcellulose affinity chromatography. The nascent RNA was hybridized to an end-labeled HindIII C probe fragment (0.646 to 0.86 map unit), and the hybrids were analyzed by S1 mapping. Most of the products of digestion corresponded to unspliced transcripts with 5' ends mapping at nucleotides 325, 260, and 195, which are positions of the 5' ends of mature, cytoplasmic late mRNA species. In addition, two minor products diagnostic of splicing at the acceptor junctions mapping at nucleotides 556 and 443 were detected. Because the abundance of these products was not diminished by repurifying the nascent RNA through a second round of sulfhydrylcellulose chromatography, these products did not originate from contaminating non-nascent RNA. Moreover, the generation of these products was not affected when a higher salt concentration and lower temperature were used for S1 digestion, conditions that should decrease artifactual cleavage by S1 in A + U-rich regions of colinear hybrids. Therefore, it is likely that some simian virus 40 RNA chains are spliced before release from the template.

Reserpine-induced alterations in mucus production and calmodulin-binding proteins in a human epithelial cell line

The characterization of a mucus-producing human cell line (HC-84) derived from a colon carcinoma and its response to in vitro reserpine treatment is reported. Mucous granules were demonstrated within these cells on the basis of electron microscopic examination and incorporation of [3H]glucosamine with subsequent autoradiographic analysis. Fluorographic analysis of total HC-84 cell protein after incubation with [3H]glucosamine indicated that the majority of tritium was incorporated into two proteins with molecular weights of 115 and 120 kD. When total HC-84 protein was subjected to immuno-blot analysis utilizing rabbit antibody against human intestinal mucus, only these two proteins (115K and 120K) reacted positively, indicating a direct correlation between [3H]glucosamine incorporation and mucus production. Immunofluorescence localization of mucus within HC-84 cells utilizing this same antibody resulted in a punctate pattern of fluorescence within the cytoplasm. Treatment of HC-84 cells with 30 microM reserpine for 7 days resulted in a three-fold increase in mucus production compared with controls. There was also a concomitant loss of a 30K calmodulin-binding protein in cells treated with reserpine. These cells represent a useful system for studying the effect of reserpine on the processes of mucus synthesis and secretion.

Nuclear beta-globin RNA transcripts initiated in vitro with gamma-thio nucleoside triphosphate

We have been able to obtain significant levels of apparently in vitro-initiated beta-globin transcripts from isolated nuclei using mouse Friend cells. The level of hybrid selected beta-globin transcripts was increased 3-9-fold in nuclei after the cells were induced with dimethylsulfoxide. The newly initiated transcripts were detected through incorporation of gamma-thio ATP and isolation by Hg-agarose chromatography. The 5'-terminus was identified by recovery of the thio tetraphosphate in hydrolysis products from in vitro initiated RNA using gamma-35S ATP.

A foreign beta-globin gene in transgenic mice: integration at abnormal chromosomal positions and expression in inappropriate tissues

We have investigated the chromosomal location, inheritance, and expression of a cloned rabbit beta-globin gene introduced into the mouse germ line by microinjection into mouse eggs. Experiments utilizing in situ hybridization to metaphase chromosomes show that the gene has integrated into one or two different chromosomal loci in each of five mouse lines analyzed. Each locus contains between three and forty copies of the foreign DNA sequence arranged in a tandem array, and the sequences at each locus are stably inherited as a single Mendelian marker. Neither globin mRNA nor polypeptides encoded by the rabbit beta-globin gene are detected in erythroid cells in the seven transgenic lines examined, indicating that the expression of the foreign gene is not correctly regulated. However, in two of the mouse lines, rabbit beta-globin transcripts are found at a low level in specific, although inappropriate, tissues: skeletal muscle in one line and testis in another line. These unusual patterns of beta-globin gene transcription are heritable traits in the two mouse lines and may result from the beta-globin gene's integration at abnormal chromosomal positions.

Posttranscriptional defects in beta-globin messenger RNA metabolism in beta-thalassemia: abnormal accumulation of beta-messenger RNA precursor sequences

The production of beta-globin messenger RNA (mRNA) in beta-thalassemic erythroblasts was studied during pulse-chase incubations with [3H]uridine. Globin [3H]mRNA was quantitated by molecular hybridization to recombinant DNA probes complementary to globin mRNA and mRNA precursor sequences. Each of six patients with beta +-thalassemia produced normal amounts of globin alpha and beta [3H]mRNA during a 20-min pulse incubation, but the beta/alpha [3H]mRNA ratio declined to steady-state levels during a chase incubation, suggesting posttranscriptional defects in beta-globin mRNA metabolism. beta-globin mRNA precursor production was estimated by measurement of [3H]RNA sequences hybridizing to a pure DNA probe containing only the large intervening sequence (intron) of the beta-mRNA precursor. Four of the patients exhibited abnormal accumulation of 3H-beta-intron sequences (2-10 times normal), indicating abnormal posttranscriptional processing. In the remaining two patients, one of whom is known to carry a mutation in the small intron of the beta-globin gene, accumulation of large 3H beta-intron RNA and beta-globin [3H]mRNA was normal in nuclei, but the ratio of beta/alpha [3H]mRNA in cytoplasm was reduced, suggesting a different posttranscriptional defect in beta-mRNA processing. These findings imply the existence of heterogeneous posttranscriptional abnormalities in beta-globin mRNA metabolism in different patients with beta-thalassemia. The initial rates of gamma- and delta-mRNA synthesis were low in all patients, suggesting that the low level of expression of these genes in adults is mediated at the transcriptional level.

Unstable beta-globin mRNA in mRNA-deficient beta o thalassemia

The molecular defect in four Kurdish Jews with homozygous, mRNA-deficient beta zero thalassemia was investigated. Electrophoretic profiles of pulse-labeled alpha- and beta-globin RNAs are similar to those of non-thalassemics; therefore, at least one of the thalassemic beta-globin alleles is transcribed. During a 30 min actinomycin D chase, most of the alpha- and beta-globin mRNA precursors and processing intermediates are converted to mRNA-sized RNA. Thalassemic and non-thalassemic beta-globin RNAs are indistinguishable, as determined by S1 nuclease mapping and RNA blotting. Non-thalassemic beta-globin mRNA is stable during a 30 min actinomycin chase, but 30%-75% of the thalassemic mRNA-sized molecules is degraded during that period. We conclude that the absence of beta-globin mRNA in this disease results from rapid turnover of beta-globin mRNA-sized molecules.

A transcription map for the rabbit beta-globin gene

We have characterized the transcripts of the beta-globin gene in RNA isolated from rabbit bone marrow using the S1 mapping procedure of Berk and Sharp (1977). The largest beta-globin-specific RNA that we have detected is a transcript, colinear with the gene, that contains the mRNA coding sequences plus both intervening sequences but does not extend into the extragenic DNA sequences. The 5' and 3' ends of this pre-mRNA maps at the same position as those of mature globin mRNA. Several partially spliced RNAs are described that are probably intermediates in the pathway from the colinear transcript to mature mRNA. The largest spliced pre-mRNA has lost only about 40 of the 126 nucleotides of the small intervening sequence and contains the entire large intervening sequence together with the coding sequences. A second major intermediate pre-mRNA lacks only the entire small intervening sequence. Finally, a pre-mRNA is described in which all but approximately 90 nucleotides of the large intervening sequence have been excised. Thus both intervening sequences appear to be able to be excised in a stepwise fashion. Removal of the small intervening sequence seems to precede the removal of the large intervening sequence.

The Role of the poly(A) sequence in mammalian messenger RNA

The poly(A) sequence is added to 3' termini of nuclear RNA segments destined to become part of the mRNA, and may play an essential role in the selection of these segments. It appears to be required for at least some of the splicing events involved in mRNA processing. In the cytoplasm, the poly(A) segment is the target of a degradation process which causes its gradual shortening, and leads to a heterogeneous steady-state poly(A)-size distribution. Complete loss of the poly(A) is probably followed by inactivation of the mRNA, since chains depleted of poly(A) do not accumulate in the cells. A role for this sequence in the promotion of mRNA stability is suggested by the behavior of globin mRNA depleted of poly(A) after injection into frog oocytes. The poly(A) shortening process may be part of the mRNA inactivation mechanism, as indicated by the greater sensitivity to degradation of the poly(A) of some short-lived mRNAs. However, the stochastic mRNA decay implies that new and old mRNA chains, with long and short poly(A) segments, respectively are equally susceptible to inactivation. The poly(A)-lacking histone mRNAs are stable only in cells engaged in DNA replication. Present knowledge favors a role for poly(A) in the control of mRNA stability. Loss of this sequence could be controlled through modulation of poly(A)-protein interactions or through masking of a sequence directly adjacent to the poly(A). In the nucleus, the poly(A) sequence could also serve as stabilizing agent, but, in addition, it might interact with the splicing machinery.

Processing of high molecular weight ovalbumin and ovomucoid precursor RNAs to messenger RNA

The existence of poly(A) sequences in the multiple high molecular weight forms of ovalbumin and ovomucoid nuclear RNA has been determined. The results indicate that all the bands observed in the total nuclear RNA including the largest (7.8 kb) were also detected in the poly(A) RNA. Kinetic labeling and chase experiments in oviduct tissue-suspension system indicated that the ovalbumin and ovomucoid high molecular weight RNAs which were labeled with a short-time incubation can be chased by cold nucleosides and actinomycin D into mature mRNAs. The largest RNAs labeled in this oviduct suspension system have a size of 7.8 kb for ovalbumin and 5.5 kb for ovomucoid, which correspond respectively to the "a" bands of steady state RNA. The processing of the precursors to mature mRNA was also examined by electron microscopic analysis, by hybridizing oviduct nuclear RNA to probes which were isolated from different segments of intervening DNA sequences and by measuring the turnover kinetics of specific intervening sequences present in cellular poly(A) RNA. The results indicate that the seven intervening sequence regions of the ovomucoid precursor are removed in a preferred but not necessarily an obligatory order.

Messenger RNA processing and nuclear structure: isolation of nuclear ribonucleoprotein particles containing beta-globin messenger RNA precursors

To explore the relationships between transcription, messenger RNA (mRNA) processing, and nuclear structure, ribonucleoprotein particles containing heterogeneous nuclear RNA (hnRNP) have been purified from globin-producing mouse Friend erythroleukemia cells. These nuclear hnRNP particles sediment at 50S-200S and contain, in addition to high molecular weight hnRNA, a specific set of nuclear proteins predominated by a major component of approximately 38,000 mol wt. The hnRNP particles are free of histones and ribosomal structural proteins, indicating their purification from the two other major nucleoprotein components of the nucleus: chromatin and nucleolar ribosomal precursor RNP particles. Th authenticity of the Friend cell hnRNP particles is demonstrated by the results of reconstruction experiments with deproteinized hnRNA, and by the resistance of the articles to dissociation during isopycnic banding in Cs2SO4 gradients without prior aldehyde fixation. Hybridization analysis with cloned mouse beta-globin DNA demonstrates that hnRNP particles from induced Friend cells contain newly synthesized transcripts of the beta-globin gene. Agarose gel electrophoresis of hnRNP particle-derived RNA denatured in glyoxal followed by "Northern" transfer to diazobenzyloxymethyl paper and hybridization with 32P-labeled cloned mouse beta-globin DNA reveals the presence in hnRNP of two size classes of beta-globin gene transcripts, the larger of which corresponds to the pre-spliced 15S beta-globin mRNA precursor previously identified in whole nuclear RNA, and the smaller of which corresponds to completely processed 9S beta-globin mRNA. These results establish, for the first time, that the nuclear transcripts of a specific, well-defined eukaryotic structural gene can be isolated in an RNP particle form, and that their RNP structure persists throughout mRNA splicing.

Addition of poly(A) to nuclear RNA occurs soon after RNA synthesis

A kinetic analysis of the appearance of [3H]uridine label in RNA sequences that neighbor poly(A), as well as the incorporation of [3H]adenosine label into both the RNA chain and the poly(A) of poly(A)-containing molecules, shows that poly(A) is added within a minute or so after RNA chain synthesis in Chinese hamster ovary cells and HeLa cells. Previous conclusions by several groups (5-7) that poly(A) might be added as long as 20-30 min after RNA synthesis appear to be in error, and the present conclusion seems much more in line with several different types of recent studies with specific mRNAs that suggest prompt poly(A) addition (13-16).

Beta Thalassemia: mutations which affect processing of the beta-Globin mRNA precursor

To define the molecular lesion which causes decreased beta-globin synthesis in beta+ thalessemia, four patients of diverse ethnic origin were studied. Each had a 2--3 fold higher concentration of beta-globin mRNA precursor than that found in control bone marrow cells from patients with sickle cell anemia. Globin RNA metabolism was analyzed in two of these patients. Transcription of the beta-globin gene appeared to be normal, since analysis of nuclear RNA indicated that beta-globin mRNA synthesis exceeded that of alpha in a 2 hr pulse but the cytoplasm contained a relative deficiency of labeled beta-globin mRNA. An abnormal RNA species approximately 650 nucleotides in length, which contained sequences transcribed from both the large intron and coding portions of the beta-globin gene, was found in one patient's bone marrow cells. The second patient's cells contained a significant amount of a 1320 nucleotide RNA species, not initially evident in normal cells, from which part but not all of the large intervening sequence had been removed. Our data thus indicate that mutations which affect RNA processing cause beta thalessemia.

Processing of human beta-globin mRNA precursor to mRNA is defective in three patients with beta+-thalassemia

Nucleated bone marrow cells from normal individuals and from three patients with homozygous beta+-thalassemia were pulse-labeled with tritiated nucleosides. The processing of the newly synthesized globin mRNA precursors was monitored by inhibiting additional transcription with actinomycin D for 30 min. Human beta-globin mRNA is derived from its precursor via a series of reactions that generate processing intermediates. In nonthalassemic cells the precursor is processed efficiently to mature mRNA during the chase. In contrast, in beta+-thalassemic cells the processing of beta-globin RNA is defective. In one patient the beta-globin mRNA precursor turns over during the chase, but some of the intermediate RNAs accumulate and are not processed to mRNA. In two other patients a large fraction of the precursor and intermediate RNAs is not processed to mRNA. The alpha-globin mRNA precursor and intermediates are processed efficiently to mRNA-sized molecules in thalassemic and normal cells. The reduction in the rate of beta-globin but not alpha-globin RNA processing accounts for the alpha/beta globin mRNA imbalance in thalassemic erythroid cells. We discuss the possibility that the genetic lesions in beta+-thalassemia are at splicing signal sites within intervening sequences of the beta-globin gene.

Bone-marrow microenvironment defect in congenital hypoplastic anemia

An abnormal bone-marrow microenvironment has been thought to have an important role in the pathogenesis of aplastic and hypoplastic anemia in some patients, but direct evidence of such a defect has not been found. We have investigated the pathogenesis of chronic anemia in a young woman. Her bone-marrow cells, obtained by means of aspiration, showed exuberant erythroid growth in methylcellulose despite marked erythroid hypoplasia. The erythroid nature of the colony growth was further confirmed through measurement of heme synthesis and messenger RNA-globin accumulation in a liquid-culture system. In contrast, when whole bone fragments were similarly cultured, no appreciable hemoglobin synthesis was observed. The experimental evidence suggests that, in this patient, hypoplastic anemia resulted from an unfavorable microenvironment.

Order of polyadenylic acid addition and splicing events in early adenovirus mRNA formation

A study of the processing of mRNA from two early adenovirus type 2 transcription units (regions 2 and 4 of adenovirus type 2 genome; [J. Flint, Cell 10:153--166, 1977]) revealed that polyadenylic acid [poly(A)] was added in most if not all cases to an unspliced nuclear RNA molecule whose coordinates extended from the apparent initiation site for RNA synthesis to the single poly(A) site in each transcription unit. An intermediate RNA molecule in the processing of the mRNA for the 72,000-M, single-stranded DNA binding protein showed that the first of the two intervening sequences, the one closest to the 5' end of the molecule, was removed first at least in the majority of the processed molecules. Finally, in cells labeled for 10 min and then treated with actinomycin D to stop further RNA synthesis, the majority, if not all, of the poly(A)-terminated nuclear RNA specific for region 2 was successfully processed and transported to the cytoplasm.

The structure and transcription of four linked rabbit beta-like globin genes

Rabbit chromosomal DNA contains a cluster of four linked beta-like globin genes arranged in the orientation 5'-beta 4-(8kb)-beta 3-(5 kb)-beta 2-(7-kb)-beta 1-3'. Determination of the nucleotide sequence of gene beta 1 confirms that this gene corresponds to the second type of two common co-dominant alleles encoding the adult beta-globin chain. With the exception of two nucleotide substitutions in the large intervening sequence (intron), the intron and flanking sequences are identical with the nucleotide sequence of the first type determined by Weissmann et al. (1979). A 14S polyadenylated transcript containing large intron sequences (possibly a mRNA precursor) is detected in the bone marrow cells of anemic rabbits. Gene beta 2 has limited sequence homology to adult and embryonic beta-globin probes and lacks a detectable mRNA transcript in the erythropoietic tissues examined. It contains at least one intervening sequence analogous to the large intron in gene beta 1. Genes beta 3 and beta 4 both contain an intron of 0.8 kb. Partial DNA sequence analysis indicates that the large intron in beta 4 is located between codons for amino acids lysine and leucine in an analogous position to that of the large intron in beta 1. In addition, a second smaller intron interrupts the 5' coding sequences of gene beta 4. Both genes beta 3 and beta 4 are transcribed in embryonic globin-producing cells. Their DNA sequence homology is limited, however, to a segment of approximately 0.2 kb located on the 5' side of the large intron.

The complete sequence of a chromosomal mouse alpha--globin gene reveals elements conserved throughout vertebrate evolution

The mammalian alpha- and beta--globin genes are thought to have evolved from a common ancestral sequence by a duplication event that occurred over 500 million years ago. We have now determined the entire nucleotide sequence of a cloned mouse alpha--globin gene, including regions that flank and interrupt the coding sequence, and have compared this sequence with the sequences of the two mouse beta--globin genes (Konkel, Tilghman and Leder, 1978; Konkel, Maizel and Leder, 1979). Like the two beta genes, the alpha gene is interrupted by two intervening sequences at precisely homologous positions, suggesting that these interruptions were present and have been preserved throughout vertebrate evolution. While the alpha and beta genes conserve considerable (approximately 55%) sequence homology in their coding regions, this homology--with certain interesting exceptions--is lost in the highly divergent flanking and intervening sequences. These exceptions are short preserved sequences positioned in such a way that they might encode signals for transcriptional initiation, poly(A) addition and RNA splicing. Furthermore, a comparison of the recently divererged beta genes and the long separate alpha gene allows us to distinguish two clearly different modes of nucleotide sequence change in evolution: a fast mode which is characterized by drastic sequence alterations involving deletions and insertions, and a slow mode which preserves sequence homology to a large extent and involves mainly point mutations.

Identification of potential ovomucoid mRNA precursors in chick oviduct nuclei

Denaturing gel electrophoresis of chick oviduct nuclear RNA reveals multiple species of RNA that are 1.5-5 times larger than ovomucoid mRNA. By analogy with ovalbumin RNA processing, these data suggest that ovomucoid mRNA is derived from a primary transcript that contains intervening sequences.

Identification of a large precursor of vitellogenin mRNA in the liver of estradiol-treated chicks

Studies were performed to determine whether vitellogenin mRNA from avian liver has a precursor molecule or not. Total cellular RNA was prepared from estradiol-treated chicken liver in the presence of 8 M guanidine HCl, 2-mercaptoethanol and aurintricarboxylic acid. After denaturation, RNA was fractionated on sodium dodecylsulfate-sucrose gradients and large size RNA was analyzed under stringent conditions on 85% formamide-sucrose gradients at 25 degrees C. RNA fractions collected from the gradients were hybridized with vitellogenin (3H)-cDNA. Besides mature vitellogenin mRNA (32S, 7,000 nucleotides) vitellogenin sequences were also found in RNA fractions ranging from 38-50S with a peak at 45-50S (12-15,000 nucleotides). Only 5-10% of the putative 38-50S pmRNA is polyadenylated. We calculated that the half-life of vitellogenin pmRNA is about 3-4 minutes. We conclude that vitellogenin mRNA has a precursor which is twice the size of the mature mRNA.

Globin messenger precursor RNA in duck immature red blood cells

A procedure is described for the chromatographic analysis of RNA under fully denaturing conditions on cross-linked Sepharose. Chromatography of DNA . RNA hybrids, poly(C) . poly(G) hybrids and complexes of poly(C) . hnRNA on Sepharose CL in pure formamide at 46 degrees C leads to denaturation and strand separation of the hybrid structures. Using this procedure, nuclear RNA from duck immature red blood cells was resolved according to molecular size and assayed for the presence of globin mRNA sequences by hybridization with complementary DNA. Two size classes of putative globin mRNA precursor molecules were detected at an elution position corresponding to 14--18 S and 23--28 S. As judged from chromatographic analysis on poly(U)-Sepharose, about 70% of the 14--18-S globin precursor RNA is polyadenylated while only 11% of the putative 23--28-S precursor RNA has a poly(A) tract. Inhibition of transcription by actinomycin D and pulse-chase experiments indicate a half-life of less than 7.5 min for these precursor RNA species.

Transcription of structural and intervening sequences in the ovalbumin gene and identification of potential ovalbumin mRNA precursors

Structural sequences that are extensively separated by nonstructural intervening sequences in the natural ovalbumin gene are coordinately expressed in target and nontarget tissue. The intervening sequences, which consist of unique sequences in the chick genome, are transcribed in their entirety. The amount of nuclear RNA corresponding to these sequences, however, is approximately 10 times less than that observed for structural sequences. The accumulation of RNA corresponding to structural and intervening sequences during acute estrogen stimulation suggests either that there are different rates of transcription for these regions of the ovalbumin gene or that RNA sequences corresponding to the intervening sequences are preferentially processed and degraded. Comparison of the in vitro expression of portions of the ovalbumin gene in nuclei isolated from chronically stimulated oviducts indicates that both structural and intervening sequences are preferentially transcribed in vitro at rates approximately 500 times greater than expected for random transcription of the haploid chick genome. In addition, electrophoresis of oviduct nuclear RNA on agarose gels containing methylmercury hydroxide reveals multiple species of RNA that are from 1.3 to over 4 times larger than ovalbumin mRNA and hybridize to both structural and intervening sequences of the ovalbumin gene. These results are consistent with transcription of the entire ovalbumin gene into a large precursor molecule followed by excision of the intervening sequences and appropriate ligation of the structural sequences to form the mature mRNA.

The precursor of mouse beta-globin messenger RNA contains two intervening RNA sequences

We have investigated the locations of the poly(A), the mRNA-specific sequences and the RNA sequences that are eventually cleaved from the 1860 nucleotide precursor of mouse beta-globin mRNA. Biochemical and electron microscopic data demonstrate that there are two intervening RNA moieties in the precursor which separate the beta-globin mRNA sequences into three portions containing 480, 205 and 155 nucleotides. One of the two intervening RNA moieties contains 780 nucleotides. The size of the smaller intervening RNA has not been determined precisely, but it is 125 nucleotides or less. The largest mRNA-specific fragment is derived from the 3' terminus of the precursor, and contains the 3' terminal poly (A) and 330 mRNA-specific transcribed nucleotides. At least one, and probably both, intervening RNAs occur within the coding portion of the mRNA sequences. The larger of the intervening RNAs is located next to the 480 nucleotide mRNA-specific fragment, and the smaller intervening RNA is located between the 205 and 155 nucleotide mRNA-specific fragments. These experiments are consistent with the notion that the intervening sequences in the DNA of mouse beta-globin genes are transcribed into the mRNA precursor and are excised from the RNA by post-transcriptional events.