The concept of mRNA abundance classes: a critical reevaluation.

Derivative plots have been constructed for hybridization reactions between polysomal poly(A)-containing RNA and oligo(dT)-primed cDNA. In one method the derivative was calculated directly from the data, and in the other, from a non-linear least squares fit using 9-10 ideal components. In some cases these methods yield very similar results and strongly suggest that the hybridization data support discrete components. Reactions with two and four major components indicate that the often-reported three abundance class model is only one of several possibilities for eukaryotic cells. In other situations neither method strongly suggests the presence of discrete components (in one case even after enrichment of the cDNA population by kinetic fractionation), implying that the components are closely spaced or that the entire mRNA population of those cells may not exist as discrete abundance classes. The universal occurrence of discrete abundance classes should be critically reexamined.     

Evidence for polyadenylated mRNA in Pseudomonas aeruginosa

In this paper, we report the synthesis of Pseudomonas aeruginosa cDNA in the presence of oligo(dT) primers. Hybridization of oligonucleotide DNA microarrays indicates that under the experimental conditions used, at least 43.7% of the expressed genes from P. aeruginosa PAO1, representing many different functional classes, can be detected by using oligo(dT)-primed cDNAs.     

Chicken histone H5: selection of a cDNA recombinant using an extended synthetic primer

We describe the use of a synthetic primer to select a cDNA recombinant clone containing H5 coding sequences. The strategy used was as follows: 1. Prepare oligo(dT) cellulose-bound mRNA from chicken reticulocytes and select 11S-18S material from sucrose gradients. 2. Use this RNA fraction both to prepare a cDNA library and as a template for H5-specific cDNA synthesis using a synthetic primer. 3. Screen out most globin cDNA recombinants with oligo(dT)-primed globin cDNA. 4. Search for H5 recombinants using H5 specific cDNA and verify the identity by DNA sequencing. Our screening suggests an H5 mRNA abundance of about two parts per thousand in chicken reticulocyte poly(A)-containing RNA. The isolation of an H5 cDNA recombinant clone is an initial step in the study of H5 genes and their relationship to H1 and core histone genes.     

Construction of cDNA libraries for highly efficient DNA sequencing from the 3' end of expressed genes

The majority of expressed sequence tag (EST) sequences available today have been derived from the 5' ends of cDNA clones. Obtaining high-quality DNA sequences from the 3' ends of oligo(dT)-primed cDNA on a large scale has been difficult because of slippage of the DNA polymerase enzyme used in direct PCR and cycle sequencing. With the completion of whole genome sequencing for more and more organisms, mRNA 3'-UTR sequences can be particularly useful for clustering large numbers of ESTs for the effective discrimination of individual genes and gene families. We have identified a flaw in the widely used oligo(dT) primers for cDNA synthesis, and here we describe an improved priming approach to effectively synthesize cDNA devoid of homopolymeric nucleotide stretches from mRNA poly(A) tails to enable highly efficient and reliable DNA sequence determination from 3' mRNA ends. Using this method, we produced a rat lung cDNA library and successfully sequenced the 3' ends of 98% of all attempted clones.     

Characteristics of rabbit globin mRNA purification by oligo(dT) cellulose chromatography

We have purified rabbit globin mRNA using oligo(dT)-cellulose and sucrose gradient centrifugation. Both α- and β-globulin mRNA molecules behave heterogeneously with respect to their elution properties during chromatography on oligo(dT)-cellulose. Those fractions eluted at the lowest ionic strength are most active in directing cell-free globin biosynthesis. By making use of hybridization with synthetic [³H]DNA complementary to globin mRNA, we have shown that this technique can be used to quantitate the extent of mRNA purification. Thus, globin mRNA is approximately 90-fold purified from reticulocyte polysomal RNA and originally constituted slightly more than 1% of the polysomal RNA. Since more than 98% of the globin mRNA sequences are bound to oligo(dT)-cellulose, we suggest that most polysomal globin mRNAs contain a poly (A)-rich region and that this region is not of uniform length nor preponderately associated with either the α- or β-globin mRNAs. In addition, we observe that the 9S globin mRNA most resistant to dissociation from oligo (dT)-cellulose is most active in directing globin biosynthesis.     

Certain properties of transcribed fragments of the mouse genome cloned in plasmid pBR322

Clones of total mouse DNA efficiently hybridized with mRNA (or cDNA) were selected by colony hybridization technique. The majority of selected fragments demonstrate hybridization with cDNA, dsRNA-B (isolated from pre-mRNA) and oligo(dT). The data obtained indicate that the base sequences hybridizing to these test-probes are contiguous within several individual cloned restriction DNA fragments. At least in two cases sequences hybridizing with cDNA belong to repetitive fraction of the mouse genome (presumptive repetitive structural genes). They are transcribed effectively, and respective mRNAs of abundant type. Two other clones contain structural genes which are expressed into mRNAs of non-abundant type.     

Sequence complexity of cDNA transcribed from a diverse mRNA population

Mouse liver poly(A)+mRNA was reverse transcribed using oligo-p(dT) or random oligonucleotides as primers to yield cDNA about equal to the mass of the template RNA. The size profile of the oligo-p(dT)-primedd cDNA was similar to that of the template RNA. RNA or cDNA driven saturation annealing of labeled single copy genomic DNA (scDNA) showed that 2% of the scDNA was complementary in either case indicating the sequence complexity of cDNA was equivalent to that of the template mRNA. These results establish for the first time that cDNA represents essentially all of the sequence complexity of a diverse template RNA population in which individual mRNA species are present in vastly different concentrations. RNA driven hydridization of the cDNA showed that about 40% of the cDNA mass represents most of the sequence complexity of the template RNA. Also, kinetics of this hybridization indicate a complexity of 58,000 kb for the template RNA, a value similar to that obtained by scDNA hybridization. We conclude that appropriately characterized cDNA probes can be used to make valid qualitative and quantitative comparisons of the complex, infrequent class mRNAs of different cells and tissues.     

Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays

Bacterial messenger RNA (mRNA) is not coherently polyadenylated, whereas mRNA of Eukarya can be separated from stable RNAs by virtue of polyadenylated 3'-termini. We have developed a method to isolate Escherichia coli mRNA by polyadenylating it in crude cell extracts with E. coli poly(A) polymerase I and purifying it by oligo(dT) chromatography. Differences in lacZRNA levels were similar with purified mRNA and total RNA in dot blot hydridizations for cultures grown with or without gratuitous induction of the lactose operon. More broadly, changes in gene expression upon induction were similar when cDNAs primed from mRNA or total RNA with random hexanucleotides were hydridized to DNA microarrays for the E. coli genome. Comparable signal intensities were obtained with only 1% as much oligo(dT)-purified mRNA as total RNA, and hence in vitro poly(A) tailing appears to be selective for mRNA. These and additional studies of genome-wide expression with DNA microarrays provide evidence that in vitro poly(A) tailing works universally for E. coli mRNAs.