Changes in the abundance of polyadenylated RNA during slime mould development measured using cloned molecular hybridization probes

Expression in Saccharomyces cerevisiae of human interferon-alpha directed by the TRP1 5' region

The complete 5' flanking region of the yeast TRP1 gene encoding N-(5'-phosphoribosyl)- anthranilate isomerase, a nonabundant protein, has been cloned and the nucleotide sequence data has been extended from -102 to -440. The CT block--CAAG structure common to all efficiently expressed yeast genes is altered in the 5' region of TRP1 and a sequence postulated to be involved in general amino acid regulation is absent. There are two possible TATA boxes at -224 and -262. TRP1, in common with HIS3, HIS4 and TRP5 has a region of dyad symmetry upstream of the coding sequence which may play a role in initiation of transcription. The relative efficiency of gene expression directed by the complete 5' TRP1 region was assessed by comparison with that of PGK by inserting a cDNA for a human interferon-alpha downstream of their respective 5' regions. The respective interferon yields indicate that their in vivo expression capabilities are a function of their 5' regions.

Transcriptional control of gene expression during development of Dictyostelium discoideum

During development of the cellular slime mold Dictyostelium discoideum, approximately 2,000 to 3,000 regulated mRNAs are induced when amoebae enter multicellular aggregates. We used in vitro transcription in isolated nuclei to follow the synthesis of individual mRNA precursors during development; these were quantitated by hybridization to cloned cDNAs or genomic DNAs. Those RNAs that are present at all stages of development--the common RNAs--were transcribed by nuclei from cells at all stages of development. By contrast, those RNAs that are present only after cells begin to aggregate--here called aggregation stage RNAs--were transcribed only by nuclei from cells at the aggregation and postaggregation stages of development. The temporal pattern of in vitro transcription correlated well with the time course of accumulation of different aggregation stage mRNAs. Continued expression of aggregation stage genes normally depends upon cell-to-cell contact or cyclic AMP (cAMP); when cells are disaggregated, the regulated mRNAs are rapidly and specifically degraded. When cAMP is subsequently added to the disaggregated cells, most of the mRNAs reaccumulate. We show here that disaggregation reduced 2- to 10-fold the relative transcription of several aggregation stage RNAs, whereas addition of cAMP to disaggregated cells reinduced the level of regulated gene transcription to values approximating those found in normal postaggregation cells. These results indicate that a representative set of Dictyostelium aggregation stage genes are under transcriptional control; both the transcription and the stability of these mRNAs require either continued cell-to-cell interactions or cAMP.

Regulation of dictyostelium discoideum mRNAs specific for prespore or prestalk cells

Prespore and prestalk cells in Dictyostelium discoideum aggregates can be separated by density gradient centrifugation. Using poly(A+) RNA from the fractionated cells to probe a cDNA library of mRNAs from postaggregation cells, we were able to identify six cDNA clones representing RNAs enriched in prespore or prestalk cells. Remarkably, transcripts of six of seven cDNA clones, previously selected to encode mRNAs present in postaggregating cells but low or absent in growing cells, also are enriched in RNA from either prestalk or prespore cells. By hybridization of cDNA probes to nitrocellulose blots of formaldehyde RNA gels, these 13 mRNA species have been examined with respect to cell type specificity, temporal pattern of accumulation, and affect of disaggregation and cAMP on accumulation. Aggregation-stage mRNAs tend to fit into three different classes. All prespore mRNAs are similar in all aspects of their regulation, while prestalk mRNAs fall into two co-regulated classes. All mRNAs that are present at significant levels during growth and differentiation are found in both cell types at comparable levels. Our results indicate that there is coordinate control of expression of genes specific for the two principal cell types.

Differences in abundance of individual RNAs in normal and animalized sea urchin embryos

A library of cDNA clones was constructed representing polysomal polyadenylated RNA of mesenchyme blastulae of Strongylocentrotus purpuratus. Using this library, we determined whether or not individual RNA species are associated with animalization of embryos by zinc ions. Clones corresponding to the most actively synthesized RNAs during the period just prior to the mesenchyme blastula stage were selected by screening colonies with in vivo-labeled RNA. The most abundant of these were chosen for further study. Individual RNA abundance was measured as percent of mass of total polyadenylated RNA by hybridizing cDNA exhaustively with cloned DNA on filters. The RNAs in the selected, cloned sequences were present in abundances of 0.01 to 1% of the mass of polyadenylated RNA. Changes in abundance of individual RNA species occurred during normal development and departures from these developmental changes occurred in the zinc-animalized embryos. Two RNA species, which normally increase 10-fold in abundance, are drastically repressed and at least one RNA species increases in abundance dramatically in the animalized embryos. These departures from the normal program of presumptive gene expression may furnish insights into changes in the normal processes of development.

Isolation and characterisation of genes for androgen-responsive secretory proteins of rat seminal vesicles

Under the influence of testosterone, rat seminal vesicles synthesise large amounts of a tissue specific protein, S. Recombinant lambda clones have been isolated containing overlapping sequences covering a 27.5 kilo base region of the rat genome within which the gene for protein S is located. Recombinant plasmids bearing cDNA sequences for protein S were constructed in pBR328. One (pcS2) contains a 690 nucleotide insert and is probably full length. Detailed restriction maps of the S-gene are presented and the structure was confirmed by analysis of R-loops and heteroduplexes. The S-gene covers a 2 kbp region of the genome and consists of a 5' intron (490 bp) separating a leading exon (120 bp) containing the 5' untranslated region from a central exon (310 bp) containing most of the coding sequence and part of the 3' untranslated region. A larger intron (1100 bp) lies within the 3' untranslated region. The cloned gene is representative of the native gene but the S gene may be heterogeneous. Using pcS2, the hormonal control of S-specific mRNA was examined and a pronounced differential response to testosterone was observed.

Use of a cDNA library for the study of mRNA changes during muscle differentiation

A cDNA library was used to measure changes in many individual mRNAs during muscle differentiation in culture. A library of 1000 clones was constructed from total myofiber poly(A) RNA. About 23% of these clones gave a detectable colony hybridization signal using end-labeled myofiber mRNA, the remainder containing muscle sequences too rare to be detected with this assay. The 230 positive clones were grouped into four classes based on relative visual intensity. Reconstruction experiments using pure globin mRNA enable us to determine the approximate percentage of total RNA made up by each mRNA hybridizing to a cDNA clone. Those clones containing sequences complementary to developmentally regulated mRNAs were identified by a differential hybridization procedure. The cDNA library was screened with end-labeled mRNA from both undifferentiated myoblasts and differentiated myofibers. Although the bulk of the clones hybridized essentially the same with both RNA populations, several dozen were found which hybridized differentially. Some clones contained sequences which were not present at all in myoblasts and present in very high quantities in myofibers. Others contained sequences found in both myoblasts and myofibers but in increased quantities in the differentiated cells. Still others contained sequences which decreased in quantity during muscle differentiation. The clones in the first group were chosen for immediate analysis since they likely contain contractile protein mRNA sequences. However, all the characterized cDNA clones can now be used as probes to study the chromosomal organization and developmental expression of genes active during muscle differentiation.

Cell-type-specific actin mRNA populations in dictyostelium discoideum

We have analyzed actin mRNA sequences present in the terminal stages of the development of Dictyostelium discoideum. Four different actin mRNA sequences were detected in migrating pseudoplasmodia. Nucleotide sequence analysis of primer-extension products derived from the four mRNA sequences showed that they each encoded an actin protein with the same eight N-terminal amino acids and that they did not derive from transcription of any previously characterized actin gene. Preculmination pseudoplasmodia of Dictyostelium contain two distinct populations of committed cells, termed prespore and prestalk cells. We show that prestalk cells contain all four of the actin mRNA sequences found in pseudoplasmodia, while prespore cells contain only three of the sequences, and mature spores contain only two. Thus there is a differential loss of actin mRNA sequences during spore-cell differentiation in Dictyostelium.

Transcriptional control of gene expression during development of Dictyostelium discoideum

During development of the cellular slime mold Dictyostelium discoideum, approximately 2,000 to 3,000 regulated mRNAs are induced when amoebae enter multicellular aggregates. We used in vitro transcription in isolated nuclei to follow the synthesis of individual mRNA precursors during development; these were quantitated by hybridization to cloned cDNAs or genomic DNAs. Those RNAs that are present at all stages of development--the common RNAs--were transcribed by nuclei from cells at all stages of development. By contrast, those RNAs that are present only after cells begin to aggregate--here called aggregation stage RNAs--were transcribed only by nuclei from cells at the aggregation and postaggregation stages of development. The temporal pattern of in vitro transcription correlated well with the time course of accumulation of different aggregation stage mRNAs. Continued expression of aggregation stage genes normally depends upon cell-to-cell contact or cyclic AMP (cAMP); when cells are disaggregated, the regulated mRNAs are rapidly and specifically degraded. When cAMP is subsequently added to the disaggregated cells, most of the mRNAs reaccumulate. We show here that disaggregation reduced 2- to 10-fold the relative transcription of several aggregation stage RNAs, whereas addition of cAMP to disaggregated cells reinduced the level of regulated gene transcription to values approximating those found in normal postaggregation cells. These results indicate that a representative set of Dictyostelium aggregation stage genes are under transcriptional control; both the transcription and the stability of these mRNAs require either continued cell-to-cell interactions or cAMP.

Differential expression of the members of the discoidin I multigene family during growth and development of Dictyostelium discoideum

Discoidin I and II are lectins synthesized during the aggregation of Dictyostelium discoideum amoebae which may play a role in cellular cohesion. Discoidin I was thought to consist of two major polypeptides, but we show that there are three. The N-terminal amino acid sequence of the polypeptides has been predicted by determining part of the nucleotide sequence of their respective mRNAs. We obtained the nucleotide sequences by reverse transcription of the mRNAs, using as primers, fragments derived from the coding region of two cloned discoidin I sequences, and utilizing cross hybridization to the various mRNA species and differences in the length of their 5' noncoding regions to isolate fragments for DNA sequencing. We used primer extension to measure the relative concentration of the three major discoidin I mRNA sequences. We show that during development changes in the abundance of all three mRNA sequences occur coordinately. In cells growing in nutrient broth, however, only two of the three major discoidin I mRNA sequences accumulate, and if such cells are grown to a very high density, both sequences disappear. These results indicate that the coordination of discoidin I gene expression is not obligatory and that the members of this multigene family may differ in the mode of their induction during normal development.

Characterization of sequence elements at the 5' end of a discoidin I gene isolated from Dictyostelium discoideum

The discoidin I genes of Dictyostelium discoideum encode a family of three closely related developmentally regulated lectins which may play a role in cell cohesion. We have isolated a genomic clone containing the 5' half of a discoidin I gene with 12kb of flanking sequence and we have identified the discoidin I polypeptide encoded by this gene. We have determined part of the nucleotide sequence of the cloned segment and have hence determined the N-terminal amino acid sequence of the encoded polypeptide. The nucleotide sequence upstream of the AUG initiation codon was unusually AT rich, with 94% AT base pairs in the 171 nucleotides for which sequence was determined. However, having determined the start point of transcription ('cap' site) two striking features of similarity with other eukaryotic structural genes became apparent. The sequence TATAAA was present 33 nucleotides upstream from the 'cap' site and the sequence CCAAT was present a further 20 nucleotides upstream.

Cloning of Xenopus laevis nuclear poly(A)-rich RNA sequences. Evidence for post-transcriptional control

cDNA/RNA hybridization experiments of polysomal and nuclear poly(A)-rich RNA from early tadpole stages of Xenopus laevis revealed that part of the nuclear poly(A)-rich RNA sequences are not present within the polysomal polyadenylated RNA. For a more detailed analysis of these sequences we have cloned double-stranded cDNA derived from tadpole nuclear poly(A)-rich RNA in the PstI cleavage site of pBR 322. By colony screening with 32P-labelled cDNA from polysomal and nuclear poly(A)-rich RNA of the tadpole stage we could identify and isolate some of the cloned sequences, which are present only within the nuclear RNA. However, hybridization with cDNA from polysomal poly(A)-rich RNA of the gastrula stage indicated that at least one of those sequences which are confined to the nucleus at tadpole stage may serve as mRNA at gastrula stage. We present evidence that nuclear and polysomal poly(A)-rich RNA molecules containing the same nucleotide sequence differ in size and that size reduction at the level of processing precedes and may enable cytoplasmic export. We conclude that, besides stage-specific regulation of transcription, post-transcriptional control mechanisms are also involved in gene expression during embryonic development.

Molecular cloning of cDNA sequences coding for the major (beta-, gamma-, delta- and epsilon-) heat-shock polypeptides of HeLa cells

The method of differential in situ colony hybridisation and the technique of two-dimensional gel electrophoresis of polypeptides synthesized in vitro by mRNAs that hybridise specifically to recombinant plasmids bound to filter discs, have been used to isolate two cDNA HeLa heat-shock clones. Each of these two clones contains the plasmid pBR322 with a cDNA fragment of about 0.3 kb inserted into the PstI site. The two fragments hae different restriction maps. Whilst one of the recombinant plasmids, pHS2, contains a cDNA sequence that hybridises to mRNA coding for the HeLa heat-shock gamma-polypeptide, the other, pHS6, cross-hybridises with mRNAs that code for the HeLa heat-shock beta-, delta- and epsilon-polypeptides.

Organization of a gene cluster expressed specifically in the asexual spores of A. nidulans

We have investigated the organization and regulation of a 13.3 kb region of the Aspergillus nidulans genome that is preferentially expressed during conidiophore development. This cloned DNA segment codes for six polysomal poly(A)RNAs present in dormant asexual spores (conidia) at from 8 to 50 copies per cell. The genes encoding these RNAs occur once per haploid genome, are separate and distinct, appear to be colinear with their mature RNA products and are present in both polarities. Two of the genes have short regions of homology near their 5' ends, but otherwise the segment is internally unique. All of the RNAs are absent from or present at very low levels in wild-type somatic cells (Hyphae) and developing cultures of asporogenous mutant strains. In synchronously conidiating wild-type cultures, each of the RNAs can first be detected at a time coinciding with the appearance of mature spores. Thus this region comprises a cluster of tightly linked, discrete genes, which are all expressed at the same time, but not to the same extent, in a single differentiating cell type.

Synthesis and stability of developmentally regulated dictyostelium mRNAs are affected by cell--cell contact and cAMP

Postaggregation Dictyostelium discoideum cells contain 3000 mRNA species that are absent from preaggregation cells; these aggregation-dependent sequences comprise 30% of the mass of mRNA in these cells. We show that the synthesis and stability of these regulated mRNA sequences are affected by both cell--cell contact and cAMP. Three independent assays are used to quantitate these mRNAs: in vitro translation followed by two-dimensional gel analysis of the protein products; hybridization of gel-separated RNAs to cloned DNAs; and hybridization of mRNA to a cDNA probe specific for the population of regulated sequences. In postaggregation cells, the half-life of both the developmentally regulated mRNAs and the constitutive mRNAs present throughout growth and differentiation is the same--about 4 hr. Following disaggregation, all of the late mRNA sequences are degraded and decay with a half-life of 25 to 45 min. The constitutive species are unaffected; 2.5 hr after disaggregation, the ratio of late to constitutive mRNAs is about 6% that of normal plated cells. Addition of cAMP to cells that have been disaggregated for 2.5 hr (or longer) restores the level of most late mRNAs within 3 hr. We conclude that cAMP stimulates the synthesis of these mRNAs and may also act to stabilize them in the cytoplasm. This effect of cAMP is dependent on the cells having been in contact with other cells; cAMP has no effect on the levels of mRNA in suspension-starved, aggregation-competent cells that have never formed cell--cell aggregates.

Selection and analysis of cloned developmentally-regulated Dictyostelium discoideum genes by hybridization-competition

We describe a new technique for selection of cloned gene segments which are expressed preferentially at one developmental stage but at a relatively low level. A nitrocellulose filter replica of plaques of lambda phage which contain approximately 8 KB inserts of genomic DNA is prepared; it is hybridized with a small amount of [32p] labeled mRNA prepared from one developmental stage, in the presence of a several-hundred fold excess of competitor RNA from a different stage. We show that clones of Dictyostelium nuclear DNA which form hybrids under these conditions indeed encode developmentally regulated mRNAs. Our previous analysis of Dictyostelium discoideum differentiation indicated that transcripts from about 12% of the genome appear in mRNA at one defined stage of differentiation - the formation of cell-cell aggregates. A number of our new clones are novel, in that they encode multiple discrete mRNA species all of which accumulate only at the cell aggregate stages; others encode one or more mRNAs which appear at the tight aggregate stage and also one or more which are present throughout differentiation. These latter clones, in particular, would be difficult to identify using other selection techniques.

A change in the rate of transcription of a eukaryotic gene in response to cyclic AMP

The plasmid pDd812 contains the DNA copy of an mRNA sequence from Dictyostelium discoideum that undergoes first an increase and then a decrease in concentration during the first few hours of differentiation. We have recently shown that the mRNA sequence complementary to pDd812 encodes discoidin I, a developmentally regulated lectin that may play a role in cellular cohesion. By using pDd812 as a hybridization probe, we found that addition of cyclic AMP during the first few hours of development inhibited the accumulation of discoidin I mRNA. By measuring the rate of transcription in isolated nuclei, we showed that, at least in part, this inhibition results from a rapid and specific reduction in the rate of transcription of the discoidin I gene. Addition of cyclic AMP during the first few hours of development inhibited the accumulation of discoidin I mRNA. By measuring the rate of transcription in isolated nuclei, we showed that, at least in part, this inhibition results from a rapid and specific reduction in the rate of transcription of the discoidin I gene. Addition of cyclic AMP during the first few hours of development inhibited the accumulation of discoidin I mRNA. By measuring the rate of transcription in isolated nuclei, we showed that, at least in part, this inhibition results from a rapid and specific reduction in the rate of transcription of the discoidin I gene. Addition of high external concentrations of cAMP is known to increase the intracellular concentration to a level normally found later in development. This natural increase in cAMP concentration occurs at the time during development when transcription of the discoidin I gene ceases. We suggest, therefore, that changes in the intracellular concentration of cAMP act at the level of transcription to control gene expression during development. This hypothesis is supported by our observation that several poly(A)+RNA sequences that normally accumulate after transcription of the discoidin I gene has ceased are synthesized prematurely in cells exposed to exogenous cAMP.

Messenger RNA prevalence in sea urchin embryos measured with cloned cDNAs

mRNA prevalence during sea urchin development was measured by treating cDNA clone colonies with labeled cDNAs transcribed from unfertilized egg and embryo poly(A)-RNAs. The number of cytoplasmic transcripts per embryo complementary to several clones was determined independently by titration with poly(A)-RNA in solution, and the amount of cDNA bound to these clones in colony hybridizations was shown to be proportional to the concentration of the respective poly(A)-RNAs in the embryo cytoplasm. At the gastrula stage, the most prevalent mRNA species occur in about 10(6) molecules per embryo. If all cells were equivalent, this would be a few hundred molecules per cell. By pluteus stage, the prevalence of some sequences has increased more than 10-fold. Most, though not all, sequences prevalent in later embryos are also present in the maternal RNA of the unfertilized egg. For most poly(A)-RNA sequences, the prevalence levels determined during oogenesis are maintained through the pluteus stage, whereas a minority of sequences display sharp stage-specific changes in representation during development.

Molecular cloning of cDNA sequences coding for the major alpha- and beta-globin polypeptides of adult Xenopus laevis

This report describes the synthesis and cloning of almost complete DNA copies of the mRNAs encoding the major alpha-globin and major beta-globin of X. laevis. Double-stranded globin cDNA was inserted into the PstI site of the plasmid pBR322 and two cloned recombinants (designated pXG6C1 and pXG8D2) were selected. These were shown to contain almost complete copies of X. laevis globin mRNA. Restriction enzyme maps were determined for each cDNA sequence using the established method of partial digestion of end labelled DNA. However, this procedure was modified such that isolation of individual DNA fragments was no longer required. Each plasmid was shown, by both hybrid arrested translation and filter selection of complementary RNA, to contain a sequence coding for one or other of the two major globin polypeptides. Sufficient DNA sequence information has been determined from each cDNA clone to demonstrate that pXG8D2 contains a beta-globin sequence and pXG6C1 contains an alpha-globin sequence.

Isolation of Trypanosoma brucei variant specific antigen mRNA by immunoprecipitation of polysomes

The mRNA encoding the variant specific antigen of Trypanosoma brucei has been prepared by immunoprecipitation of polysomes. Polysomes carrying the variant specific antigen account for approx. 3% of the total polysomes. The mRNA thus produced is active in the mRNA dependent rabbit reticulocyte lysate in vitro protein synthesis system and directs the synthesis of a polypeptide of 60 000 daltons which co-migrates both with 125I-labelled purified variant specific antigen and with antigen immunoprecipitated from reticulocyte lysate charged with total polyadenylated mRNA from the same clone. The mRNA is being used both to prepare cDNA clones and to prepare high specific radioactivity cDNA to be used to screen a gene bank for clones containing variant specific antigen coding sequences.

Characterization of cloned cDNA sequences derived from Xenopus laevis poly A(+) oocyte RNA

Double-stranded cDNA sequences were prepared from Xenopus laevis ovary poly A(+) RNA with AMV reverse transcriptase and nuclease S1. They were inserted into the plasmid pBR 322 after ligation with a Hind III linker and were cloned in E. coli strain X1776. Plasmid pools containing a cDNA insert were identified by Hind II restriction and hybridization of the DNA fragments with radiolabelled pBR 322 DNA. Hybridization of the positive pools with ovary RNA labelled in vitro led to the identification of cloned cDNA sequences which represent RNA species of high to intermediate abundance in the ovary. Positive clones were further challenged with in vitro labelled mitochondrial DNA and RNA from different developmental stages. One clone of mitochondrial origin has been detected. The hybridization characteristics of the cDNA sequences with the RNA probes from later developmental stages is discussed.