Physical parameters affecting the rate and completion of RNA driven hybridization of DNA: new measurements relevant to quantitation based on kinetics

DEVELOPMENT OF AN EVANESCENT FIELD SYSTEM FOR REAL-TIME DETECTION OF DNA HYBRIDIZATION

In this research, we report the characterization of the probe and target oligonucleotide hybridization reaction using the evanescent field microscopy. For detection of DNA hybridization assay, a high-density array of sensor probes were prepared by randomly distributing a mixture of particles immobilized with oligonucleotides for DNA chip applications. With the evanescent field excitation and real-time detection method, we suggest that a very sharp discrimination of bulk fluorescence against surface excitation in combination with high excitation intensities can be achieved.

Optimization of the rate of DNA hybridization and rapid detection of methicillin resistant Staphylococcus aureus DNA using fluorescence polarization

The hybridization rate of two complementary single-stranded DNA 24-mers was determined at various NaCl concentrations using a fluorescence polarization method. The rate was taken as the rate constant of the second order reaction, obtained by mathematical fitting of the time course curves of hybridization. The rate increased with the NaCl concentration, plateauing in the concentration range of about 1-2 M. Over the temperature range of 46 degrees C to 56 degrees C, it was found that in 0.8 M NaCl, hybridization was complete in under 10 min and that the difference in the polarization values between specific hybridization and non-specific binding was greater at lower temperatures. Under the optimized conditions of 0.8 M NaCl at 46 degrees C, the time for DNA hybridization to reach 90% completion decreased to less than 5 min. The assay time for one sample was 10 min and the detection limit was of the order of 10(-10) M (40 fmol per assay). Under the optimized conditions, the DNA of methicillin resistant Staphylococcus aureus (MRSA), which had been multiplied by PCR, could be detected within 10 min.

High throughput RNase protection assay

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The impact of the PCR plateau phase on quantitative PCR

The quantitative use of the polymerase chain reaction (PCR) is often compromised by the variability of the amplification. The most useful system for quantitation by PCR involves the use of controls which are almost identical to the target and which can be amplified using the same primers as the sequences of interest. In this paper, we use a model system consisting of differently sized targets amplifiable with varying primers to demonstrate the effects of the plateau phase of PCR on quantitation by PCR. This model confirms two commonly observed results: (i) when varying amounts of a single target are amplified, a constant maximum level of product is obtained and (ii) coamplification of different concentrations of different targets results in retention of the initial proportions. The inherent contradiction in these results is examined by replacement of the key elements of the reaction including enzyme, dNTPs or primers, none of which have an effect on the plateau. Pyrophosphate is found to exert no inhibitory effect on the reaction, nor does the exonuclease action of the enzyme cause the plateau. Levels of amplification attained during amplification are both theoretically and empirically defined as being insufficient to lead to the plateau due to competition between self-annealing of product DNAs and primer binding. We conclude that, pending further biochemical enquiry into the enzyme(s) used in the PCR, none of reasons conventionally proposed for the plateau phase of the PCR are sufficient to explain the phenomenon. This being so, we define the plateau as being a feature of the reaction as a whole and, since the onset of this phase is simultaneous for all amplicons, quantitation using the internal control system need not require exponential amplification. This therefore greatly simplifies the quantitative application of PCR.

Construction and characterization of a normalized cDNA library

We have developed a simple procedure based on reassociation kinetics that can reduce effectively the high variation in abundance among the clones of a cDNA library that represent individual mRNA species. For this normalization, we used as a model system a library of human infant brain cDNAs that were cloned directionally into a phagemid vector and, thus, could be easily converted into single-stranded circles. After controlled primer extension to synthesize a short complementary strand on each circular template, melting and reannealing of the partial duplexes at relatively low C0t, and hydroxyapatite column chromatography, unreassociated circles were recovered from the flow through fraction and electroporated into bacteria, to propagate a normalized library without a requirement for subcloning steps. An evaluation of the extent of normalization has indicated that, from an extreme range of abundance of 4 orders of magnitude in the original library, the frequency of occurrence of any clone examined in the normalized library was brought within the narrow range of only 1 order of magnitude.

Identification of cDNA clones expressed selectively during the critical period for visual cortex development by subtractive hybridization

We have used the method of subtractive hybridization to isolate cDNA clones of mRNAs expressed in abundance in the visual cortex of 30-day-old kittens but absent or in lower abundance in the adult cat visual cortex. Of 12,000 colonies screened, 200 clones which hybridized to the subtracted probe were isolated and characterized. Northern blots confirmed the specificity of the vast majority of the isolated clones. 120 of the 200 clones were sequenced and the EMBL and GenBank (release 76) database were searched for known identities using FASTA and BLAST programs. Twenty-seven of these sequenced clones were identifiable. The identities showed that these sequences code for proteins involved in a variety of cellular processes. These include cell-cell interaction (TAPA-1, contactin, tachykinin receptor, phospholipase A2), cellular remodeling (C1q beta isoform, heat shock protein), neurofilament assembly (alpha tubulin and alpha internexin), neurotransmitter release (VAMP-2, amphiphysin, carboxypeptidase E, scg 10 and proton channel), energy metabolism (mitochondrial hinge protein, ADP/ATP transporter, cytochrome oxidase subunits), RNA processing (helix destabilizing protein, ribonucleoprotein) and protein synthesis (eIF-4A initiation factor, ribosomal protein S27). The results show that gene expression in the kitten visual cortex differs rather little from that of the adult visual cortex since over 98% of the sequences appear common. The relatively rare kitten-specific sequences are likely to form the basis for the critical period plasticity in this system.

Leucine aminopeptidase: an inducible component of the defense response in Lycopersicon esculentum (tomato)

A leucine aminopeptidase (EC 3.4.11.1) cDNA clone (DR57) that was induced in response to Pseudomonas syringae pv. tomato (P.s. tomato) infection was isolated using a subtractive hybridization-enriched cDNA probe. Genomic DNA blot analysis showed that the tomato genome had two leucine aminopeptidase genes. The levels of DR57 mRNAs after P.s. tomato infection and mechanical wounding were determined in two inbred tomato lines that exhibit susceptibility and resistance to P.s. tomato. DR57 mRNAs were detected 12 hours after infection and 4 hours after wounding. Furthermore, DR57 mRNAs were systemically induced in response to wounding. DR57 mRNAs were induced in leaves after Spodoptera littoralis feeding but were not detected in detached leaf controls. Possible roles for the DR57 leucine aminopeptidase in the defense reactions are discussed.

A new approach to understanding T cell development: the isolation and characterization of immature CD4-, CD8-, CD3- T cell cDNAs by subtraction cloning

During T cell development in the mammalian thymus, immature T cells are observed that lack the cell surface markers CD4, CD8, and CD3. A subtracted cDNA library was constructed to isolate cDNAs that are specific for these immature T cells. Tissue-specific expression of 97 individual cDNAs were examined using different cell types by Northern blot analysis, and six cDNAs were analyzed by reverse transcriptase (RT) polymerase chain reaction (PCR) detection of RNA. Approximately 50% of the clones could not be detected on Northern blots, and 40% of the clones were expressed by at least one other cell-type including monocytes, mature T cells, and B cells. Eight cDNA clones appear to be specific for the CD4-, CD8-, CD3- T cell line, used to construct the library, as determined by Northern blot analysis. In addition, 330 cDNA clones were subjected to partial automated DNA sequence determination. Database searches, with both nucleotide and protein translations, revealed cDNAs that exhibit interesting similarities to human cell-cycle gene 1, platelet-derived growth factor receptor, c-fms oncogene (CSF-1) receptor, and members of the immunoglobulin gene superfamily. This approach of employing subtraction coupled with large scale partial cDNA sequence determination can be useful to identify genes that may be involved in early T cell growth, cellular recognition or differentiation.

Isolation and characterization of a library of cDNA clones that are preferentially expressed in the embryonic telencephalon

In order to isolate genes involved in development of the mammalian telencephalon we employed an efficient cDNA library procedure. By subtracting an adult mouse telencephalic cDNA library from an embryonic day 15 (E15) mouse telencephalic cDNA library we generated two subtracted libraries (ES1 and ES2). We estimate that ES1 contains between 200 and 600 different cDNA clones, which approximates the number of genes that are preferentially expressed in the E15 telencephalon, compared to the adult telencephalon. Northern analysis of 20 different cDNA clones shows that 14 of these are expressed at least 5-fold more in the E15 telencephalon than the adult telencephalon. Limited sequencing of the 14 differentially expressed clones reveals that 10 have no significant identity to sequences in GenBank and EMBL databases, whereas the other 4 have significant sequence identity to vimentin, histone 3.3, topoisomerase I and the B2 repeat element. In situ hybridization using one of the differentially expressed cDNAs, TES-1, demonstrates that it is transiently expressed in the anlage of the basal ganglia. In situ hybridization with another differentially expressed cDNA clone, TES-4, shows that it is specifically expressed in differentiating cells of the neural axis with a distinctive rostral-caudal temporal pattern. These findings, and the methods that we have developed, provide a framework for future investigations of the genetic control of telencephalon development.

DNA probes: applications of the principles of nucleic acid hybridization

Nucleic acid hybridization with a labeled probe is the only practical way to detect a complementary target sequence in a complex nucleic acid mixture. The first section of this article covers quantitative aspects of nucleic acid hybridization thermodynamics and kinetics. The probes considered are oligonucleotides or polynucleotides, DNA or RNA, single- or double-stranded, and natural or modified, either in the nucleotide bases or in the backbone. The hybridization products are duplexes or triplexes formed with targets in solution or on solid supports. Additional topics include hybridization acceleration and reactions involving branch migration. The second section deals with synthesis or biosynthesis and detection of labeled probes, with a discussion of their sensitivity and specificity limits. Direct labeling is illustrated with radioactive probes. The discussion of indirect labels begins with biotinylated probes as prototypes. Reporter groups considered include radioactive, fluorescent, and chemiluminescent nucleotides, as well as enzymes with colorimetric, fluorescent, and luminescent substrates.

Early Changes in Gene Expression during the Transition from Vegetative to Generative Growth in the Long-Day Plant Sinapis alba

Changes in gene expression during flower formation were studied in the long-day plant Sinapis alba. The day length dependence was exploited to synchronize flower formation in a large population of mustard plants. After an inductive light treatment, apices were harvested after different lengths of time, and changes in gene expression were analyzed. Two major groups of genes were identified whose expression was affected during flower formation. Transcripts of the first group (group I) were present at low concentration in the apex of noninduced plants. They began to accumulate strongly after the end of the inductive light period. They reached a maximum 2 days to 10 days after flower induction and then declined slowly. Transcripts of the second group of genes (group II) could be detected for the first time 10 days after flower induction. Within a very short time, these transcripts accumulated dramatically and reached a maximum 15 days after flower induction before beginning to decline. They dropped beyond the limit of detection before the flower reached maturity.

Early Changes in Gene Expression during the Transition from Vegetative to Generative Growth in the Long-Day Plant Sinapis alba

Changes in gene expression during flower formation were studied in the long-day plant Sinapis alba. The day length dependence was exploited to synchronize flower formation in a large population of mustard plants. After an inductive light treatment, apices were harvested after different lengths of time, and changes in gene expression were analyzed. Two major groups of genes were identified whose expression was affected during flower formation. Transcripts of the first group (group I) were present at low concentration in the apex of noninduced plants. They began to accumulate strongly after the end of the inductive light period. They reached a maximum 2 days to 10 days after flower induction and then declined slowly. Transcripts of the second group of genes (group II) could be detected for the first time 10 days after flower induction. Within a very short time, these transcripts accumulated dramatically and reached a maximum 15 days after flower induction before beginning to decline. They dropped beyond the limit of detection before the flower reached maturity.

Effect of monovalent cation-induced telomeric DNA structure on the binding of Oxytricha telomeric protein

Oligonucleotides bearing 4 repeats of telomeric deoxyguanosine-rich sequence undergo a monovalent cation-induced transition to a folded conformation with G-G base pairs, modeled as a 'G-quartet' structure. We have now deduced the rates of folding and unfolding of d(TTTTGGGG)4, which has four repeats of the Oxytricha telomeric DNA sequence. The estimated average values of delta G for the folded form at 37 degrees C are -2.2 kcal/mol and -4.7 kcal/mol in 50 mM na+ and K+, respectively. The fully folded DNA is not recognized by the Oxytricha telomere-binding protein; the substrate for protein binding has properties consistent with its being partly or fully unfolded. In confirmation of this conclusion, prevention of DNA folding by methylation enables the protein to bind as rapidly in the presence of monovalent cations as in their absence. The slow unfolding (t1/2 = 4 hr and 18 hr at 37 degrees C in Na+ and K+, respectively) of the DNA suggests that such structures would be long-lived if they formed in vivo, unless they can be actively unfolded. The inability of the telomere-binding protein to bind the stable, folded form of the 4-repeat telomeric sequence is a problem that may be circumvented in vivo by avoiding four single-stranded repeats.

Low-ratio hybridization subtraction

A hybridization subtraction protocol that uses low ratios of RNA to cDNA has been developed to enrich for the cDNA of transcripts that are elevated in one cell population relative to another. This low-ratio hybridization subtraction protocol was found to yield substantial enrichment for the cDNA of low-abundance transcripts induced or increased only several fold. Conditions for the cloning of cDNA enriched by our hybridization subtraction and identification of clones coding for induced transcripts are presented. By screening the cDNA library with probes synthesized from the starting cDNA and cDNA enriched by low-ratio hybridization subtraction, clones coding for induced transcripts could be efficiently identified. The choice of reverse transcriptase used to synthesize the cDNA was found to be important for the enrichment of cDNA for longer length RNA. Low-ratio hybridization subtraction of cDNA synthesized with MMLV reverse transcriptase was effective for the enrichment of cDNA coding for RNA to at least 5 kb in length, while the AMV enzyme was effective only for the cDNA of shorter RNA (less than 1 kb). The characterization of several different low-ratio hybridization subtraction libraries is presented, and the advantages and disadvantages of various hybridization subtraction strategies are discussed.

Amplified RNA synthesized from limited quantities of heterogeneous cDNA

The heterogeneity of neural gene expression and the spatially limited expression of many low-abundance messenger RNAs in the brain has made cloning and analysis of such messages difficult. To generate amounts of nucleic acids sufficient for use in standard cloning strategies, we have devised a method for producing amplified heterogeneous populations of RNA from limited quantities of cDNA. Whole cerebellar RNA was primed with a synthetic oligonucleotide containing the T7 RNA polymerase promoter sequence 5' to a polythymidylate region. After second-strand cDNA synthesis, T7 RNA polymerase was used to generate amplified antisense RNA (aRNA). Up to 80-fold molar amplification has been achieved from nanogram quantities of cDNA. The amplified material is similar in size distribution to the parent cDNA and shows sequence heterogeneity as assessed by Southern and Northern blot analysis. Specific messages for moderate-abundance mRNAs for actin and guanine nucleotide-binding protein (G-protein) alpha subunits have been detected in the amplified material. By using in situ transcription to generate cDNA, sequences for cyclophilin have been detected in aRNA derived from single cerebellar tissue sections. cDNA derived from a single cerebellar Purkinje cell also has been amplified and yields material that hybridizes to cognate whole RNA and mRNA but not to Escherichia coli RNA.

Forebrain-enriched RNAs of the canary: a population analysis using hybridization kinetics

Canaries and other songbirds offer unique advantages for analyzing the relationship between specific gene regulation and neural plasticity. To establish a quantitative profile of the population of RNAs potentially involved in this regulation, we analyzed the solution hybridization kinetics of canary forebrain cytoplasmic polyadenylated RNA. Hybridization of forebrain cDNA to forebrain RNA provides evidence for RNA species at individual concentrations ranging from less than 10(-6) to about 10(-3) (by fractional mass). Cross-hybridization to RNA from the rest of the brain, together with other studies, defines a subpopulation of about 5000 rare RNAs that are enriched in the forebrain compared to the rest of the brain. Some of these forebrain-enriched RNAs are likely to play a role in regulating the neural plasticity characteristic of the canary forebrain.

Myogenin, a factor regulating myogenesis, has a domain homologous to MyoD

In this report, we describe the isolation, sequence, and initial characterization of the cDNA for the muscle-specific regulatory factor skeletal myogenin. Transfection of myogenin into the mesenchymal cell line C3H10T1/2 produces cells expressing muscle-specific markers. Myogenin is absent in undifferentiated cells, peaks, and then declines following a stimulus to differentiate, and is overexpressed in myoblasts selected with 5-bromodeoxyuridine for the overproduction of factors that regulate the decision to differentiate. High levels of myogenin transcripts are present in the myotomal region of somites at 8.5 days of gestation in the mouse. Although myogenin and MyoD are different genes, they share the myc homology domain. Myogenin and MyoD thus form part of a gene family regulating myogenesis, and together with myd may constitute a set of factors that interact to regulate the determination and differentiation of muscle cells.

Probes for rare mRNAs reveal distributed cell subsets in canary brain

cDNA clones of 7 low-abundance canary brain RNAs hybridize in situ to different subsets of brain cells. Although these cell sets are distinct, they are dispersed in a variety of brain regions with overlapping anatomical distributions. These cDNA clones were initially selected by their relative hybridization to forebrain and rest-of-brain RNAs and represent a sampling of a much larger population of differentially expressed RNAs present at individual concentrations of 10(-7) to 10(-4) as a fraction of polyadenylated RNA mass. Our results suggest the existence of several thousand low-abundance brain mRNAs likely to be distributed in diverse and overlapping brain cell subsets. Furthermore, our experiments define a simple and general strategy for producing and analyzing molecular probes for subsets of brain cells and provide an initial set of useful reagents for further study of brain organization and development.

A hybridization and enzyme blocking method to enrich minor cDNA sequences

A method is presented which allows for the enrichment of low frequency cDNA sequences. The crucial step in the procedure is the hybridization of a pool of cDNA to homologous or heterologous RNA to a Rot value which will leave minor sequences in a single strand cDNA form while the major sequences form cDNA:RNA hybrids. This allows subsequent enzymatic differentiation between major and minor sequences resulting ultimately in the degradation of the major sequences. The procedure is general and simple as it requires no column chromatography step. The method is designed to integrate into a widely used cDNA cloning protocol and results either in double-stranded cDNA which can be used for molecular cloning or as a source of probes for hybridization.

Regulation of gene expression by ethylene during Lycopersicon esculentum (tomato) fruit development

We have investigated the regulation of gene expression by the plant hormone ethylene by cloning mRNAs that accumulate in unripe tomato fruit (Lycopersicon esculentum) exposed to exogenous ethylene. The response to exogenous ethylene is rapid; within 30-120 min we detect an increase in the cloned mRNA concentrations. DNA sequence analysis indicates that one of the ethylene-inducible genes is related to a gene encoding wound-inducible proteinase inhibitor I. We have measured ethylene production during fruit development and detect low basal levels in unripe fruit and much higher levels in ripening fruit. Blot hybridization experiments show that expression of the cloned genes is developmentally regulated by ethylene during fruit ripening: the mRNAs produced by these genes are more abundant in ripe fruit than in unripe fruit, and this mRNA accumulation is repressed by a competitive inhibitor of ethylene action, norbornadiene. However, during fruit development some of the cloned mRNAs begin to accumulate when ethylene production is at a basal level, whereas other mRNAs begin to accumulate later when the endogenous ethylene concentration increases, suggesting that gene expression during fruit development can be activated by ethylene in two ways. In some cases gene expression is primarily activated by an increase in sensitivity to basal ethylene levels, whereas in other cases it may be regulated by an increase in ethylene concentration.

An efficient approach for the selective isolation of specific transcripts from complex brain mRNA populations

As a consequence of the complexity of the nervous system, many characteristic proteins are only expressed at low levels, and their detection and purification often represents a formidable task. A strategy based on liquid hybridizations, which greatly facilitates the identification of the mRNA transcript for this kind of protein, is presented here. A ten-fold-enriched recombinant library was generated from cDNA transcribed from forebrain mRNA after subtraction of cerebellum sequences. Clones specific to forebrain could then be revealed with cerebellum subtracted probes, by colony hybridization. The use of selected cDNA populations greatly enhanced the sensitivity of the screening procedure; clones corresponding to transcripts present at an abundance as low as 0.0005% could still be detected. About 5% of specific clones were recognized with an enriched forebrain probe. Additional clones were revealed with subtracted probes from restricted areas such as cerebral cortex, brainstem, and hippocampus. The important features and potential applications of this approach are discussed.

A generally applicable improved method for preparation of single stranded cDNA probes from clones constructed in M13 vectors

A generally applicable simplified procedure for the preparation of radiolabeled cDNA hybridization probes from cDNA clones in M13 (M13mp8) bacteriophage vectors is described. A cDNA copy of the insert DNA is synthesized by controlled reaction with the Klenow fragment of E. coli DNA polymerase I, primed with oligo-dT or sequencing primer. The cDNA is separated from the recombinant phage DNA template by alkaline gel electrophoresis. Sensitivity of the cDNAs was tested by quantitative measurement of specific mRNAs in solution hybridization under RNA (R0t analysis) or cDNA (RNA titration) excess conditions. The procedure permits measurement of mRNA levels as small as 0.00001-0.00006% in total RNA preparation. Cellular accumulation of hormone-induced mRNAs for the milk proteins, whey acidic protein and epsilon-casein was also measured using the cDNAs.

Detection of sickle-cell mutation by electrophoresis of partial RNA:DNA hybrids following solution hybridization

We have developed a method in which partially single-stranded (ss) DNA molecules containing a defined region of duplex RNA:DNA are electrophoretically separated in agarose gels. The partial hybrids are formed by solution hybridization with a uniform length RNA probe complementary to part of the DNA sequence of interest. Following hybridization, the RNA/DNA mixture is fractionated by agarose gel electrophoresis at high temperature to minimize intrastrand base pairing which causes mobility heterogeneity. Not requiring the steps of DNA transfer from the gel to a solid support and subsequent probing, pre-electrophoretic hybridization allows the direct identification of single-copy fragments. Conditions for the detection of single-copy genes in human DNA digested with specific restriction endonucleases were developed and applied to the diagnosis of sickle-cell disease. This method should be applicable for the analysis of DNAs of high complexity where the presence of DNA polymorphisms and interspersed repeated DNA sequences often make impossible the creation of complete RNA:DNA hybrids.

Interstrand duplexes in Friend erythroleukemia nuclear RNA. The interaction of non-polyadenylated nuclear RNA with polyadenylated nuclear RNA and with small nuclear RNAs

Intermolecular duplexes among large nuclear RNAs, and between small nuclear RNA and heterogeneous nuclear RNA, were studied after isolation by a procedure that yielded protein-free RNA without the use of phenol or high salt. The bulk of the pulse-labeled RNA had a sedimentation coefficient greater than 45 S. After heating in 50% (v/v) formamide, it sedimented between the 18 S and 28 S regions of the sucrose gradient. Proof of the existence of interstrand duplexes prior to deproteinization was obtained by the introduction of interstrand cross-links using 4'-aminomethyl-4,5',8-trimethylpsoralen and u.v. irradiation. Thermal denaturation did not reduce the sedimentation coefficient of pulse-labeled RNA obtained from nuclei treated with this reagent and u.v. irradiated. Interstrand duplexes were observed among the non-polyadenylated RNA species as well as between polyadenylated and non-polyadenylated RNAs. beta-Globin mRNA but not beta-globin pre-mRNA also contained interstrand duplex regions. In this study, we were able to identify two distinct classes of polyadenylated nuclear RNA, which were differentiated with respect to whether or not they were associated with other RNA molecules. The first class was composed of poly(A)+ molecules that were free of interactions with other RNAs. beta-Globin pre-mRNA belongs to this class. The second class included poly(A)+ molecules that contained interstrand duplexes. beta-Globin mRNA is involved in this kind of interaction. In addition, hybrids between small nuclear RNAs and heterogeneous nuclear RNA were isolated. These hybrids were formed with all the U-rich species, 4.5 S, 4.5 SI and a novel species designated W. Approximately equal numbers of hybrids were formed by species U1a, U1b, U2, U6 and W; however, species U4 and U5 were significantly under-represented. Most of these hybrids were found to be associated stably with non-polyadenylated RNA. These observations demonstrated for the first time that small nuclear RNA-heterogeneous nuclear RNA hybrids can be isolated without crosslinking, and that proteins are not necessary to stabilize the complexes. However, not all molecules of a given small nuclear RNA species are involved in the formation of these hybrids. The distribution of a given small nuclear RNA species between the free and bound state does not reflect the stability of the complex in vitro but rather the abundance of complementary sequences in the heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of the Complexity and Diversity of mRNAs from Pollen and Shoots of Tradescantia

The mRNAs of the mature pollen grain of Tradescantia paludosa at anesthesia and of vegetative shoots have been compared by analyzing the kinetics of hybridization between homologous and heterologous reactions of cDNA to poly(A)RNA in excess. The mRNAs in pollen can be divided into three abundance classes with complexities of 5.2 x 10(4), 1.6 x 10(6), and 2.1 x 10(7) nucleotides. The three classes are made up of sequences that constitute 15, 60, and 24% of the mRNAs and each sequence is present on an average at 26,000, 3,400, and 100 copies, respectively, per pollen grain. About 20,000 different genes are expressed in pollen as compared to about 30,000 in vegetative shoots. Estimates have been made of pollen mRNA sequences shared with those of shoot tissue and of shoot sequences common to those in pollen.

Organ-specific nuclear RNAs in tobacco

We investigated the developmental regulation of nuclear RNA sequences in tobacco vegetative (leaf, root, stem) and floral (petal, ovary, anther) organ systems using RNA-excess X single-copy DNA hybridization reactions. We found that 18% of the single-copy DNA, equivalent to 1.1 X 10(5) kilobases (kb) of diverse transcripts, is represented in the nuclear RNA of each organ. Each nuclear RNA population has both shared and organ-specific sequences. Depending upon the nuclear RNA, 10-40% of the complexity, or 1.1-4.4 X 10(4) kb of diverse sequence, is organ-specific. Collectively, at least 45% of the single-copy DNA, or 3 X 10(5) kb, is represented in the nuclear RNA of the entire plant. Hybridization experiments with polysomal RNA showed that organ-specific mRNAs are present in both the unique and shared nuclear RNA subsets. Together, our results show that tobacco nuclear RNA sequences are under striking developmental control and that both transcriptional and post-transcriptional processes play a role in regulating plant gene expression.

Changes in gene expression during postnatal development of the rat cerebellum

The base sequence complexity of total and polysomal poly(A +)RNA from rat cerebellum was measured during postnatal development by RNA-DNA hybridization. At saturation, total and polysomal poly(A +)RNA from neonate cerebellum hybridized to 12.7% and 5.0% of the single-copy genomic DNA, respectively. Assuming asymmetric transcription, the sequence complexity of these RNA populations is sufficient to code for greater than 100,000 different gene transcripts. The percentage of single-copy DNA expressed as total and polysomal poly(A +)RNA declined during postnatal development, reaching adult values of 10.0% and 4.1%, respectively. These results indicate that cerebellar maturation is accompanied by significant reductions in the diversity of genetic information expressed in the tissue.

Genetic expression in the developing brain

The adult mouse brain contains complex populations of polyadenylated [poly(A)+] and nonpolyadenylated [poly(A)-] messenger RNA's (mRNA's). These mRNA's are separate sequence populations, similar in complexity, and in combination are equivalent to approximately 150,000 different mRNA sequences, of average length. Essentially all of the "adult" poly(A)+ mRNA's are present in the brain at birth. In contrast, most of the poly(A)- mRNA's are absent. Brain poly(A)- mRNA's begin to appear soon after birth, but the full adult complement is not reached until young adulthood. This suggests that these poly(A)- mRNA's specify proteins required for the biological capabilities of the brain that emerge during the course of postnatal development.