To appear on Bioinformatics, Vol 2: 93-105, 1999.
A computer-driven approach to
PCR-based differential screening,
 alternative to differential display
Department of Biological and Technological Research (DIBIT),
 San Raffaele Scientific Institute (HSR), Via Olgettina 58, 20132 Milano, Italy
and RICCARDO FESCE * (email)
DIBIT-HSR and Consiglio Nazionale delle Ricerche, Cytopharmacology Center

Running head: Computer-driven RNA Fingerprinting

Keywords: Genetics, Computer Simulation, Sequence Analysis, Differential Display, RNA Fingerprinting

Motivation: PCR-based RNA fingerprinting is a powerful tool for the isolation of differentially expressed genes in studies of neoplasia, differentiation, or development. Arbitrarily primed RNA fingerprinting is capable of targeting coding regions of genes, as opposed to differential display techniques, which target 3' noncoding cDNA. In order to be of general use and to permit a systematic survey of differential gene expression, RNA fingerprinting has to be standardized and a number of highly efficient and selective arbitrary primers must be identified.
Results: we have applied a rational approach to generate a representative panel of high-efficiency oligonucleotides for RNA fingerprinting studies, which display marked affinity for coding portions of known genes and, as shown by preliminary results, of novel ones. The choice of oligonucleotides was driven by computer simulations of RNA fingerprinting RT-PCR experiments, performed on two custom-generated, nonredundant nucleotide databases, each containing the complete collection of deposited human or murine cDNAs. The simulation approach and experimental protocol proposed here permit the efficient isolation of coding cDNA fragments from differentially expressed genes.
Availability: Freely available on request from the authors.
    The analysis of differential gene expression focuses on molecular mechanisms involved in major biological processes, such as cell differentiation, cell division, embryonic development, neoplastic transformation and growth. A multitude of techniques has become available in recent times to isolate differentially expressed genes (see, e.g. Fargnoli, Holbrook and Fornace, 1990; Ausubel et al., 1995; Velculescu et al., 1995; Diatchenko et al., 1996). In 1992, Liang and Pardee first described a new, differential screening technique, based on Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), which they named Differential Display (DD)  (Liang and Pardee, 1992). In this technique, cDNAs are synthesized by means of anchored oligo-dT primers, to select subsets within given mRNA populations. First strand cDNAs are subsequently PCR-amplified using the same downstream oligo-dT primer and an upstream random decamer. The complex PCR product is fractionated through a polyacrylamide gel and detected by autoradiography thanks to the incorporation of a radioactive dNTP in the PCR reaction. The technique aims at revealing bands corresponding to differentially expressed genes from a background of constitutively expressed products. Various refinements of the above protocol have been published (Bauer et al., 1993; Consalez et al., 1996; Hadman et al., 1995; Liang, 1994; Liang and Pardee, 1995; Rohrwild et al., 1995; Tokuyama and Takeda, 1995; Zhao, Ooi and Pardee, 1995). However, products obtained from DD gels derive almost exclusively from noncoding regions of genes, whose sequence analysis provides no cues regarding protein function.
    A different RNA display protocol was developed by Welsh et al. (1992), to permit internally primed PCR amplification of cDNAs. In this protocol, named RAP-PCR, only arbitrary primers are used in the radioactive PCR amplification step. Unlike DD, arbitrarily primed RNA fingerprinting has not been approached systematically to maximize coverage of genes expressed in mammalian systems within a finite number of PCR amplifications. In other words, no rationally designed panel of primers is available for a fairly exhaustive survey by RAP-PCR of gene expression in a given biological system.
 We have recently developed a modified RAP-PCR protocol featuring highly reproducible banding patterns, marked efficiency and sensitivity, and a nonrandom affinity for coding regions. This protocol has allowed several research groups to isolate differentially expressed genes from various model systems ranging from rodents to humans (Corradi et al., 1996; Malgaretti et al., 1997; Cabibbo et al., 1998; Guttinger et al., 1998; Covini et al., in press; Dragoni et al., in press; Mariani et al., in press; Rossetti et al., in preparation).
    In this paper, we describe a computer analysis of human and mouse cDNA databases aimed at selecting a panel of the best primers to use in our approach. A similar, but distinct strategy was proposed by Lopez-Nieto and Nigam (1996). The collection of reagents generated through our approach and the technical updates described here make us able to propose internally primed, PCR-based RNA fingerprinting as a reasonably simple, systematic tool for the analysis of differential gene expression, and as a workable, advantageous alternative to differential display.
Simulation of mRNA PCR in nucleotide (nt) databases - PCR simulations were run on two nonredundant (nr) databases, obtained from a combination of human or mouse sequences deposited into the Genbank and EMBL nucleotide sequence databanks (accessed through the GCG Wisconsin package, version 8.1-UNIX, August 1995) (Devereux, Haeberli and Smithies, 1984). One arbitrary 12-nt primer sequence was used at a time, i.e. each primer was assumed to anneal in a degenerate fashion to both the sense and antisense strand.
    The nr human and mouse databases were obtained by selecting human or mouse entries containing at least 1000 bp of coding sequence (CDS). In order to decrease redundancy, variable regions of immunoglobulins and T-cell receptors were eliminated, and all pairs of sequences sharing a word in their product descriptions were compared by the FASTA algorithm (Pearson, 1994); the shorter one was eliminated when >95% identical to the other. Intronic regions were eliminated from genomic sequences, thereby generating new transcribed sequence files containing uninterrupted cDNA.
    Annealing of the primers was simulated by searching both strands in the nr databases for the sequence of each primer, by means of the FINDPATTERNS program in the Wisconsin GCG package, permitting a maximum of 3 mismatches. All pairings with one or more mismatched base(s) among the last 4 (at the 3' end) were excluded as not suited to prime a polymerase chain reaction (PCR). A simulated PCR product was scored whenever a pairing occurred on the sense strand and, 100-1000 bp downstream, on the antisense strand.
    For each primer, simulated PCR products were tagged with a CDS flag, if they contained any amount of coding sequence, or with a UTR flag, if they only contained a portion of 5' or 3' untranslated region. Each primer could be attributed an "efficiency" score (total number of simulated PCR products in the sequence database) and a "selectivity" score (percentage of the simulated PCR products at least partially comprised of coding sequence). All simulations were performed using a Sun Workstation; the procedures used for generating nr sequence databases and simulating RT-PCR are freely available.
    A crucial aspect in assessing the validity of the approach proposed here is to exclude that differences in "efficiency" observed among random primers be fortuitous. Thus, the distribution of the number of products per primer, obtained through the simulation experiments, was compared to the one calculated for a randomly scrambled sequence database, considering that (i) all primers were constituted by 8 G's or C's and 4 A's or T's, (ii) each sequence in the databank had a certain proportion of G's or C's and (iii) a perfect match was required for 4 bases at the 3' end, whereas up to 3 mismatches were allowed over the first 8 bases from the 5' end of each primer. The computations of the expected product number distribution are described in Appendix I and were performed with the Matlab software (Matworks, Natik, MA) on a personal computer.
Standard molecular techniques - All standard molecular techniques employed in this paper were performed as described in Current Protocols in Molecular Biology (Ausubel et al., 1995).
RNA fingerprinting - Total RNA's were extracted in duplicate by the cesium chloride method (Sambrook, Fritsch and Maniatis, 1989), digested with 4 IU DNase, phenol-chloroform extracted, ethanol-precipitated and resuspended. From 1 µg of each duplicate total RNA sample, reverse transcriptions (RT) were carried out with a (dT)16 primer. From 10 µl of a 1:10 dilution of each RT product, radioactive PCR reactions were performed in 50 µl final volumes with single 12-mer primers (final conc. 4 µM); 1.5 mM final [MgCl2]; 200 µM final [dNTP]. PCR conditions were as follows: 3 min. at 94 °C, 2 min. at 80 °C when 2.5 IU Taq polymerase (Perkin Elmer) was added (hot start), followed by 35 cycles of 1 min. at 94 °C, 1 min. at 50 °C, 1 min. at 72 °C, with a final elongation step of 5 min. at 72 °C. 0.1 µl [a32P]dCTP (3000 Ci/mmol) or 0.2 µl [a33P]dCTP (1000-3000 Ci/mmol) were added to each reaction mix. Amplification products were separated on 5% denaturing polyacrylamide gels and visualized by autoradiography. Differentially displayed bands were cut from gels and DNAs electroeluted overnight at 60V in dialysis bags. Bands were reamplified using the same 12-mer primers as in the RNA fingerprinting experiment, and cloned into the EcoRV site of pBluescript II SK (Stratagene), as previously described (Consalez et al., 1996). Clones corresponding to differentially displayed bands were selected from the background of unrelated products, as described (ibidem).
Sequence analysis of cloned products - Data bank searches (Genbank, GenEmbl, SwissProt and PIR) were run through the BlastN and BlastX network servers (Altschul et al., 1990). Additional sequence analysis was done using the GCG package (ver. 9.0).
Computer simulations

    Computer simulations of RNA fingerprinting PCR experiments were run on custom made human and murine nonredundant (nr) nucleotide databases generated as described in the Systems and Methods section.

Simulations in a human database - In a first series of simulations (MAN12.8) 10,000 12-character strings were generated at random, to represent dodecanucleotide primers, with the initial requirement that they contain 8 C's or G's and 4 A's or T's, reflecting higher C and G contents in coding regions than in 3' untranslated regions. Primers containing either stop codons (TAA, TAG, TGA) in the sense strand or ³ 4 homonucleotide stretches (AAAA, CCCC etc.) were discarded (criteria a and b, respectively). Also discarded were primers with palindromic 5' and 3' ends, ³ 4 successive complementary bases long (criterion c). The above criteria were aimed at biasing the primers towards the coding sequences (CDS, a), and at enhancing the efficiency of PCR experiments (b and c).
    The first 1,000 primers considered acceptable according to criteria a, b, and c, were challenged against the human nr database (2,085-sequences, 4.4 Mb total DNA, 72.8% CDS, see Materials and Methods), to simulate the PCR. Primers yielding >100 but <250 simulated PCR products were considered adequate (114 primers); 345 primers were labeled as inefficient and 44 as "too efficient" (primers yielding an excessive number of products might target repetitive or low complexity templates, and result in low amplification efficiencies in the experimental phase); 497 primers were excluded because they contained >5 out of 8 bases at the 3' end identical to a previously accepted primer (criterion d). This criterion was aimed at reducing the chance of repeatedly targeting the same sequences.
    Figure 1A illustrates a histogram of simulated PCR product numbers obtained with the series of 503 accepted primers based on criteria a-d. Also illustrated is the probability density function (%) computed for the same set of primers against a randomly scrambled sequence database (see the Appendix for details on the computation of this curve). The observed distribution is nonrandom, featuring markedly overcrowded shoulders. This indicates the existence of significant numbers of particularly inefficient primers, as well as of particularly efficient ones, and points to the possibility of selecting a panel of valuable PCR primers based on the present "simulated gene fishing" approach.
Simulations in a mouse database - The same panel of 1000 primers, generated for simulations in the human database, was tested on the mouse nr nucleotide database (MOUSE 12.8), containing 1041 sequences comprised of 2.95 Mb total nucleotide sequence, (72.5% CDS), in order to check whether species-specific features in sequence composition played a major role in determining the efficiency scores of different primers. In this case, 193 "good" primers and 326 inefficient or too efficient ones were obtained; 481 primers were excluded due to criterion d. The distribution of simulated PCR product numbers per primer was qualitatively similar to the one obtained in the human database. Figure 1B is a scatter plot of the number of simulated PCR products obtained in the human (x-axis) vs. the mouse (y-axis) database, with the same primers. The two sets of values correlate very well (correl. coeff. r = 0.947).


Degree of coverage of the primer panel - Next, we set out to address the issue of exhaustivity of a panel comprised of the 96 best primers. It may be argued that the primers selected because of their high efficiency in yielding simulated PCR products may be directed towards subpopulations of genetic sequences within the expressed sequence database. If this were the case, the number of transcripts not targeted by any primer (failures) should be higher than expected based on the mean number of simulated products per transcript. Figure 1C describes a simulation run on the human nr database and illustrates that this is not the case. In particular, it shows the number of primers targeting each transcript. The 96 most efficient primers yield more products in the actual transcribed sequence database than it can be calculated for a randomly scrambled transcribed sequence database. When such increase in efficiency is taken into account, theoretical distributions (dashed lines in figure 1C) fit the results of the simulations, arguing against a bias of our primer panel towards specific subpopulations of target sequences. Basically, our data speak for the existence of good and bad primers (nonrandom distribution), but fail to reveal the existence of unexpectedly good or bad templates (random distribution).

Effect of base composition of the primers - The choice of primers rich in C's and G's was driven by the goal of targeting coding regions. However, it became necessary to ascertain whether this unbalanced base composition in the primers could determine a bias in the choice of target sequences from the database. To address this issue, the same simulations described above were performed using 12-nucleotide primers composed of 6 A's or T's and 6 C's or G's (MAN12.6, MOUSE12.6). As far as coverage, the results were superimposable to those obtained with the CG-rich primer set (not shown).

Use of degenerate primers - We reasoned that the introduction of a partially degenerate position at the 3' end of each primer would lead to an increase in product numbers, and enhance the exhaustivity of our optimal primer collection. Thus, we went back and repeated computer simulations using 12-nucleotide CG-rich primers, containing a partially degenerate base (W or S) at their 3' ends (representing primer pairs, rather than single primers). As expected, the use of degenerate primers in simulations gave rise to an increased product number, with respect to nondegenerate ones (figure 2A). 


Efficiency vs. selectivity for coding regions - The selectivity for coding sequences was examined together with the efficiency in yielding high numbers of simulated PCR products. In particular, 522 degenerate primers were tested and the panel of 96 "best" ones was generated by assigning an efficiency index (EI) and a selectivity index (SI) to each primer. The EI reflects the efficiency in yielding PCR products in general (that is the total product number), while the SI reflects the affinity of a primer for coding regions (that is the ratio of coding region products to total number of products). See Appendix for computation of EI's and SI's. Degenerate primers with an EI between 0.3 and 1.18 (i.e. a product number 2 to 15 times the modal value) and an SI greater than 1.4 were selected (figure 2B). The 96 degenerate primers with the highest SI's were grouped in the "best primers" panel (table 1).

  Table 1
ID. sequence  S.I.  E.I. ID. sequence  S.I.  E.I. ID. sequence  S.I.  E.I.
942  ACGCCATCGACC/G 6.39  1.84 280 GCCGGGAACTTC/G  2.34  5.9  192 AGCCGGAGGATG/C 1.81  7.5 
688  AAGCTGCTCGCG/C 4.99  2.07 103 ATCCTGCACCGC/G  2.33  3.28 745 AGAGTGCGCTCG/C 1.79  2.77
522  GGCACATTGCGG/C  4.5  1.96 529 AGGTACCCGTGC/G 2.31  4.98 112 CCTGCCGGAAGA/T 1.79  6.94
567  CCAGATGCCCGA/T  4.44  2.06 445 TGTTGTGGCGGC/G 2.3  3.01 952 CAGGCCACATCG/C 1.76  2.74
328  GCAGCATCCGGA/T  3.86  2.75 701 CGGCTATCGGCT/A  2.28  2.2  791 TCCTGCGGATCG/C  1.76  2.98
60  CGATCACAGCGG/C 3.63  2.28 302 GCGGACCTCATG/C  2.27  7.68 164 CAGGTCACGGAG/C  1.74  7.74
95  TCGATGCCGCTG/C  3.35  8.03 212 CTCTCCGATGCC/G  2.26  3.7  918 CCGGAAAGCACG/C 1.74  2.51
417  ATGGCAACGGCG/C 3.32 5.77 237 CCGGGTCCTCAT/A  2.24  6.79 108 CTTGGTCGTGCC/G  1.72  2.71
TCTGGGAACCGG/C  3.19  2.65 115 GGCGCCTACTTC/G  2.23  5.09 292 CGTGCAGTTCCC/G  1.71  3.55
187  TGCTGCAGGACC/G  3.17  7.61 674 CGGCTTTCGTGC/G  2.16  2.22 372 TCTCCGCGGTCA/T  1.71  4.27
88  CGTGGGCAACCT/A  3.13  6.9  20  ATGCCCAAGCGC/G 2.13  2.11 799 AGACCGTGGACG/C 1.7  2.33
814  GAGCTTCACCGC/G  3.13  2.32 470 CAGCAAGTCGGC/G 2.09  2.81 366 GAGGAACCGGAC/G 1.68  10.69
780  GAGGCGACGATC/G 3.1 3.92 176 AAGCCGACCTCC/G 2.08  5.79 286 GACCACCGTGTG/C 1.68  6.21
402  TCGTCGACGGTG/C  3.08  1.89 156 GCGCATCCAGCT/A  2.08  14.82 355 CCAGCGTGTTCC/G  1.68  2.12
282  ACAGGCGATGCC/G 3.08  3.06 109 GGCATTCCGCAC/G 2.04  4.32 910 CACCTACCGAGC/G 1.66  2.57
648  AGAGCAGGGCGA/T 2.93  2.01 320 GCACCGACTGGT/A 2.02  9.16 418 CCAACGAGTCCC/G 1.65  2.45
91  CTTCTCCCGGTC/G  2.8  4.82 137 ACCAAGCCCACC/G  1.99  11.2 114 CTGGTCACGTGC/G  1.64  3.88
685  TGTGGAGCCGGT/A  2.79  2.38 138 CCTGTCCGTCCT/A  1.93  18.49 224 CCCGTCTACCAC/G  1.63  12.37
151  CGGCACATCTCC/G  2.68  4.95 230 GGTCCCAATGGG/C  1.93  10.68 313 GCCCTTCGTCAG/C  1.63  5.53
333  GGCCGCATTGGA/T  2.66  6.48 357 GTCCTGCGGGTT/A  1.92  1.91 149 CACAACCGGCAG/C 1.63  10.82
97  GCAGAAGCCGTG/C 2.64 2.6 423 AGCGGAGCATCC/G  1.92  1.91 453 GTGCCACGCATC/G  1.62  2.6 
29  CGGTCATGGTCG/C  2.58  2.26 283 AGCTCTGCGAGC/G  1.91  7.73 119 GCTCGATCAGGC/G  1.6  6.3 
309  GGCCGAAGACCA/T  2.57  5.91 23 CCGCATGTCCAC/G  1.9  19.46 542 AGGACGCGCATC/G 1.6  3.12
850  CCAGCACTTCGC/G  2.54  2.17 560 CGCCCTGGAACT/A  1.9  3.07 580 TGGCCAACTGCG/C 1.59  3.93
468  AGCCATTCGGGC/G  2.53  2.86 868 GTCGCCGGCAAT/A 1.89  1.83 185 TCGTCACCAGCC/G  1.59  6.81
80  GTGTTGGTGCCC/G  2.47  7.53 755 GCTGCCGCCAAT/A  1.88  3.52 463 GTGGACGGTGCA/T  1.59  6.2 
180  TGGACGTTGGCC/G  2.42  8.05 219 CGCTGTCGAGGA/T  1.87  5.99 132 TCGTGGCTGCAG/C 1.58  12.19
24  GGAGAAGCTGCC/G 2.39 10.91 595 AGGGCTTTCGGC/G  1.87  2.34 290 GCCTCCTGGAGT/A 1.56 
824  AGGCGGACATCG/C 2.35  2.82 130 GGTGCTCAGCAG/C 1.85  15.4 56 TGGCTGGGATGG/C  1.54  8.4 
195  AGCAGCTCGTGG/C  2.35  8.91 96 CCTTGGAAGCCC/G  1.82  8.35 332 GCGGATGCGGAA/T  1.53  4.02
52  CAATACGGGCCC/G  2.35  1.97 507 GCGGTCGAAGAC/G 1.82  4.33 163 ACGTGCCCAGCA/T  1.53  11.55
511  ACAAGGGCACGG/C 2.35  1.87 324 TCTGCCGGGTCT/A  1.82  6.8  51 TGCCGACTCTGC/G  1.51  15.7
Table 1 - 96 primers selected for their high efficiency in yielding large number of PCR products, expressed as efficiency index (E.I.), and for their selectivity for coding regions versus untranslated regions of transcripts, expressed as selectivity index (S.I.). See text and appendix for the significance and computation of the two indices. 

     Our data show that the distributions of product numbers per transcript, obtained by employing the 96 best degenerate primers, are shifted to the right with respect to expectations calculated for a database of scrambled cDNA sequences. The same applies to the number of primers targeting each transcript (figure 2C). This evidence confirms that the 96 best primer set is particularly efficient. The expected distributions, once corrected for the efficiency ratio (dashed curve in figure 2C, see Appendix), reasonably agrees with the observed distributions. Again, this argues against the existence of good or poor templates for our primer set; in other words, the primers fail to exhibit a bias towards a subset of genes in the database.
Coverage vs. redundancy - A series of simulations with different parameters were run to investigate the exhaustivity and redundancy of the approach proposed here. Simulations were run on either the human or the murine nr cDNA databases. Selected panels of 12-base primers with either 6 or 8 G's or C's out of 12 were employed. In some simulations, the whole set of primers was tested, and in some a maximum of only two mismatches was allowed in the simulated annealing process. Figure 3 illustrates the relationship observed between the mean number of products per transcript and the number of failures (transcripts not targeted by any primer) in 9 simulations. It can be noticed that the number of no-hits (lack of exhaustivity) decreases as the mean number of products per transcript (redundancy) increases. However, the decrease is much slower than expected based on simple Poisson statistics, and 90% coverage is reached at the cost of a redundancy factor of 10. The failure rates are in agreement with the expectations computed for scrambled databases when all primers are used (empty triangles), while they significantly decrease when high-efficiency primers are employed.


 Experimental assessment of the primer panel

    As a result of the elaboration described above, 25 primers were synthesized and tested at the bench (12 nondegenerate, 13 degenerate), to assess the correspondence between theoretical predictions and experimental results. As templates, we used total RNA from HepG2 cells cultured in different redox conditions (Cabibbo et al., in preparation), and from embryonic and postnatal mouse brain territories (Corradi et al., in preparation; Alli et al., in progress).

Setup of optimal amplification conditions - The optimal annealing temperature for our primer panel was determined by testing different annealing temperatures in a range between 45 °C and 53 °C. The best results were obtained at 50 °C. Lower temperatures caused weaker, fuzzier banding patterns, whereas no bands were seen with 52 or 53 °C in the annealing step. The optimal number of degenerate nucleotides was also determined experimentally, by testing primers containing no degenerate position, one degenerate position at the 3' end nucleotide, or two degenerate positions at nt 11 and 12. The best and most reproducible results were repeatedly obtained with one site of partial degeneration (W or S) at nt 12, or the 3' terminal nucleotide.

Annealing of the primers to the target sequences - As a further step, we analyzed the mode of annealing in our experimental conditions with respect to the annealing constraints set in our simulations. Clones obtained by RNA fingerprinting were sequenced and aligned to nucleotide databases. Products identical to deposited cDNAs or ESTs were analyzed to determine where exactly in the transcript the primer had annealed, with how many mismatches, and where the mismatches had occurred in the primer sequence. As shown in figure 4A, the experimental annealing conditions represent an excellent approximation of the simulated ones. In only two cases out of twenty nine did a mismatch occur at any site within the last four bases at the 3' end of the oligonucleotide. As it turns out, in all other cases the last four bases of the primer and template matched perfectly, defining a 3' four-base stretch critical for annealing and elongation when using a 12mer in our PCR conditions. Throughout the remaining length of the primer, annealing could occur even in the presence of up to four mismatches.


Correlation of theoretical and actual PCR product numbers - What can be inferred from the analysis of our simulations is not the total number of products to be expected in each experiment. This value is affected by a cohort of experimental variables, including the complexity of the gene pool in a given tissue and the stringency of experimental conditions. In fact, one goal of the present study was to establish general criteria useful to predict the relative efficiency of each computer-generated oligonucleotide sequence based on the frequency of its occurrence in transcribed and translated regions.
    To this end, we proceeded to counting the numbers of bands observed in RNA fingerprinting gels performed with some of the primers generated as described above. An extremely conservative approach was adopted in counting bands: only clearly distinct products evident after overnight exposure were taken into account. Our data suggest that the use of the radioactive tracer [a32P]dCTP as opposed to [a33P]dCTP results in a significant underestimate of product numbers, giving rise to fuzzy, overlapping bands. The mean number of bands obtained by using each of 12 nondegenerate primers was 66; the mean number of bands obtained by using each of 13 degenerate primers was 111, a significant increase in efficiency. While on a purely statistical basis the introduction of one partially degenerate nucleotide is expected to yield an approximately 4-fold increase in product numbers in our system, a lower increase was observed experimentally, probably due to limiting factors in the PCR reaction. When our data were arranged in the form of a scattergram (figure 4B), a positive correlation could be observed between theoretical expectations and relative experimental efficiencies. In particular, the correlation indicates that primers expected to be efficient always give rise to a high number of products (absence of false positives), whereas some of the primers expected to work poorly do in fact perform well in the experimental phase (presence of false negatives). Extrapolating these preliminary data, it can be inferred that a differential screening study employing the best 96 primers in our collection should permit a survey of over 10,000 bands. An estimate of the coverage provided by this figure is dependent upon the degree of redundancy and the complexity of the gene pool in each given tissue or cell line. At this stage, an experimental assessment of redundancy is of limited significance, due to the small number of products analyzed so far.

Selectivity of primer panel for coding sequences - Thirty three "differentially displayed" bands obtained by RT-PCR with each of nine different twelvemers were cloned and sequenced, 29 of which displayed ORFs throughout their lengths. Of these, 20 represented known coding sequences or their homospecific/cross-specific homologues; 9 additional new ORFs were analyzed with the GRAIL program (Roberts, 1991), which predicted an excellent coding probability in 6 out of nine cases. The relatively low number of cloned and sequenced products makes it impossible to correlate expected and observed ratios of coding to noncoding cDNAs and, in fact, the ratio of coding to noncoding cDNAs reflects that of translated to untranslated RNA sequence in mammalians. However, it may certainly be inferred from these preliminary results that the internal primer panel described here enhances access to coding regions by two orders of magnitude when compared to the differential display approach.

Size of amplified cDNAs - Because the described amplification strategy is based on the occurrence of two copies (one sense and one antisense) of a degenerate 12-mer within a single mature transcript, we set out to determine whether our approach would lead to the preferential amplification of large size cDNAs, corresponding to large transcripts. Table 2 describes the sizes of transcripts and open reading frames from 13 published cDNAs identified through our approach. These transcripts range in size between 1.0 and 3.8 kb. The corresponding open reading frames range in size between 582 and 1914 nt. These preliminary figures suggest that small transcripts are amplified as efficiently as larger ones, likely due to (i) high levels of degeneracy in the primer annealing step, and (ii) high-frequency occurrence of specific sequence motifs in coding regions.

    Table 2.
gene name
mRNA (kb)
CDS (bp)
Ref. or GB accession #
Rossetti et al., in preparation
Dragoni et al., in press
Covini et al., in press
Cytokeratin 17
Thioredoxin reductase
Table 2 - Transcript sizes (mRNA kb) and open reading frame lengths (CDS bp) for 13 published cDNAs identified through the approach here described. A histogram of open reading frame lengths illustrates their distribution.

    The basic idea of computer assisted gene fishing, illustrated here, is to select, among random-sequence PCR primers, the most efficient and selective ones, as judged from the results of computer simulations of PCR procedures on nonredundant cDNA sequence databases. The simulation approach represents a forceful oversimplification of experimental conditions and is governed by rigid rules: in the case described here, hybridization was assumed to occur whenever a perfect 4-base match at the 3' end of the primer occurred, with no more than 3 mismatches in the remaining portion, and a relevant PCR product was assumed to occur whenever a pairing occurred on the sense strand and a second pairing occurred on the antisense strand, 100-1000 bp downstream. These assumptions overlook the occurrence of (a) highly degenerate annealing on particularly abundant mRNA species, which can yield detectable bands in PCR gels; (b) hairpins generating gaps in primer-template doublets; (c) limiting PCR reagent concentrations which may disfavor mRNA species present at low copy numbers. Still, the results reported here support the value of simulation as a rational approach to designing efficient and selective primers for RNA fingerprinting.
    The notion of employing 12-bp PCR primers selected according to criteria other than pure chance is supported by several lines of evidence. Experimentally, large differences are observed in the number of PCR products generated from the same cDNAs by "high efficiency" versus "low efficiency" primers. It is well known that the frequency of occurrence of nucleotide "words" of a given length varies widely among different types of DNA sequences (introns, coding regions, etc.) (Claverie, Sauvaget and Bougueleret, 1990). This suggests that specific 12-nt sequences, when used as PCR primers, may be endowed with widely different efficiencies and possibly selectivities for coding vs. non-coding regions. Indeed, all simulations indicate that the distributions of the number of simulated PCR products per primer markedly depart from the ones computed for a randomly scrambled database (probability density function). A large excess of particularly efficient and particularly "poor" primers was observed in all simulations, which confirms the notion that the proposed approach might help in selecting particularly favorable 12-nt primer sequences for RNA fingerprinting. When the significance of these findings is assessed by challenging the same set of primers against the human and murine sequence databases, the numbers of PCR products obtained in the two simulations correlate very well, indicating that the unexpectedly high or low efficiencies of some primers do not arise from aberrations in the composition of the databases used, but rather from intrinsic differences in efficiency among primers. In other words, this confirms that some "genetic words" have particularly high or low probabilities of occurring in coding sequences (Claverie, Sauvaget, and Bougueleret, 1990), with no major differences between phylogenetically related genomes.
    The predictivity of simulation in selecting efficient primers appears to be confirmed by the analysis of the number of PCR products experimentally obtained with a reduced panel of primers. The actual probability of hybridization under the experimental conditions described was obviously unknown, as were the exact sizes of the cDNA pools analyzed. The absolute numbers of PCR products were lower than in the simulations; however, the relative efficiencies of the tested primers were in reasonable agreement with our predictions.
    A series of criteria were adopted in selecting the random-sequence primers to be tested by PCR simulation. These criteria were aimed at excluding primers which would likely generate technical problems (e.g. those containing homo-nucleotide stretches), at biasing the primers towards coding regions (a fixed ratio of 8 C's or G's to 4 A's or T's was used, and primers containing stop codons in the sense strand were excluded) and at obtaining exhaustivity (at least four out of eight nt at the 3' end were unique for each selected primer). The last constraint turned out to be quite restrictive, in that after selecting about one hundred primers many further random sequences had to be generated in order to find a new, compatible one. Conceivably, this may lead to an enhanced coverage by our primer panel.
    As reported above, most of the PCR products cloned so far using the primers in the panel contain significant ORFs, either throughout their whole lengths, or at one end. This supports the idea that a panel of primers selected as described here should make it possible to address coding regions in mRNA in a majority of cases, permitting a prediction as to the nature of corresponding peptide sequences, and the establishment of cross-specific relationships with deposited sequences from distant phyla. Although an increasing number of transcribed sequences are deposited in nucleotide databases, catalogs are only complete for one model eukaryotic organism, and a long time may elapse before full length cDNAs become available for a significant number of organisms. Likewise, in the case of large genomic sequences deposited in the framework of organism-specific genome sequencing projects, the availability of a coding sequence tag would circumvent the need for the lengthy and error-prone process of identifying and splicing transcribed sequences at the computer. Thus, the prompt recognition of a newly discovered sequence as a member of a phylogenetically conserved gene family represents a significant advantage of our approach over previously described ones. The results described here are more relevant when one considers that, in its current version, our protocol utilizes oligo-dT-primed first strand cDNA, thus shifting the cDNA pool towards 3' ends. An experimental update in our approach will require first strand cDNA synthesis using internal primers, rather than oligo-dT primers, to further enhance targeting of coding sequences. To date, this has not been done lest a significant portion of products might contain ribosomal RNA sequences, and is the current subject of methodological work by our group.
    An additional question to address was whether the primers selected because of their high efficiency in yielding simulated PCR products were directed towards subpopulations of genetic sequences. Three criteria were considered: (i) the relation between the length of the sequences and the number of products they yielded showed no sign of clustering into subpopulations (not shown); (ii) the distributions of the number of simulated PCR products per sequence never displayed multiple modes and were generally smooth and continuous; (iii) although such distributions were shifted towards high numbers of products (especially when obtained with the sets of 96 best-performing primers) with respect to the expectations for scrambled sequence databases (Appendix), they were well fit by simply increasing the matching probability by a factor equal to the ratio [observed / expected] mean numbers of products; the latter approach also yielded adequate predictions of the percentage of non-targeted transcripts ("silent sequences"). All this argues against the existence of subpopulations of nt sequences with significantly different probabilities of being recognized by the sets of primers employed here.
    A more difficult problem to tackle is redundancy, i.e. the production of many amplification products from each transcript in the mRNA library used. A balance between redundancy and exhaustivity must be reached empirically. In our simulations, the percentage of "silent sequences" was closely approximated by the reciprocal of the mean number of products from each sequence (a measure of redundancy). Our data suggests that, as the number of products increases, the proportion of "silent sequences" decreases more slowly than expected from Poisson statistics, where the fraction of failures is predicted by exp(-mean). The departure from Poisson behavior, observed in the simulations, is predicted theoretically, based on the heterogeneous probability of being sampled for sequences with dissimilar length and composition. An experiment employing 96 primers with some 100 bands per primer would yield about 10,000 discernible PCR products; assuming that a typical cell expresses some 20,000 genes, this would correspond to an average hitting rate of 0.5 PCR products per expressed gene. According to our theoretical predictions and simulations, under this conditions coverage should approximate 13% (as opposed to the theoretical upper limit of  39% for a purely random, Poisson distribution). Thus, the method here proposed is certainly not aimed at obtaining exhaustive coverage of differential gene expression. Much higher numbers of primers (and PCR products) would be needed; for example, in order to fish out 90 % of the 20,000 expressed genes one should analyze about 200,000 bands. Classical differential display with similar numbers of PCR products should obtain similar coverage rates, since available data suggest that the probability of yielding PCR products by differential display is also markedly heterogeneous (genes expressed in high number of copies have much higher probability of yielding PCR products; Bertioli et al., 1995; our unpublished data). Thus, the main differences should not regard coverage, but bias at low coverage levels: whereas differential display tends to produce PCR products for more abundantly expressed genes, the approach here proposed appears not to be biased in this regard and to produce a high percentage of PCR products in coding regions.
    An approach similar to ours has been taken by others (Lopez-Nieto and Nigam, 1996). Those authors proposed and described a protocol employing each one of 30 computer-generated arbitrary 8-nt primers selected for their probability of occurrence in sense strands of coding sequences, to be used in combination with each of the reverse complement series, i.e. 29 primers. In the present paper, we propose the utilization of single, partially degenerate primers selected for their frequent and balanced appearance both in sense and antisense strands. The protocol proposed by Lopez-Nieto and Nigam entails the use of 30 ´ 29 = 870 PCR amplifications, as opposed to 96 in our schema. Although 870 primer combinations will provide greater coverage of the genes expressed in a given tissue sample than just 96 PCRs, from our analysis of the relationship between exhaustivity and redundancy, one would suspect that the gain may not be worth the effort (2-3 times as many expectedly targeted genes). More in general, we believe that one should probably not embark on a PCR-based differential screening project with the goal in mind of producing a complete catalog of differentially expressed genes; instead, a more sensible scope would be to generate a number of genetic tags helpful in initiating the dissection of functional pathways in development or differentiation active in one's system of choice. As a matter of fact, these pathways typically involve, in addition to differentially expressed genes, ubiquitously expressed genes as well as post-transcriptional and post-translational regulatory events. Other valuable, albeit more demanding approaches are available to those researchers who wish to generate complete catalogs, rather than obtaining a sample of differential gene expression in their biological systems (Kato, 1995). More importantly, microchip-based technology will become more generally available in the medium term for high-throughput, genome science-style studies in many organisms.
    At difference with Lopez-Nieto and Nigam’s study (1996), which described computer analysis for a large set of random primers, but focused on the experimental validation of a primer set specifically designed to target a group of G protein-coupled receptor genes, the present study has identified primers not biased towards any specific gene family, which have been utilized experimentally by a number of groups to target protein coding regions in general, and all appear to work equally efficiently in the standard experimental conditions described in the present paper (Corradi et al., 1996; Cabibbo et al., 1998; Malgaretti et al., 1997). Furthermore, the octamers need 5' adaptors to increase product numbers and high annealing temperatures (54 °C) to decrease the background of low-efficiency/truncated amplification products (Lopez-Nieto and Nigam 1996). However, this procedure might somewhat favor the recursive amplification of sequences partially or completely homologous to the adaptor. Our protocol employs longer primers, at a lower annealing temperature (50 °C), resulting in good control of the background level, and high amplification efficiencies.
    The evidence presented here demonstrates that, in our scheme, only four residues at the 3' end of our primers need to anneal with a perfect match to their templates for the polymerase chain reaction to take place, while up to four mismatches are well tolerated over the remaining eight residues. Thus, 12-mer primers such as the ones proposed in the present paper produce large numbers of products in our experimental conditions by virtue of partially degenerate annealing. Furthermore, as primer sequences used in experiments are identical to those used in simulations (no adaptors), effective lessons on how to refine the simulation strategy can be learned from the analysis of experimental results.
 In summary, the present approach, by combining the predictive power of computer-based database analysis with the establishment of robust, repeatable experimental conditions, proposes PCR-based RNA fingerprinting as a rejuvenated, efficient approach to the analysis of differential gene expression.

We thank Carol L. Stayton and Nicoletta Malgaretti for their essential contribution to the described protocols. This methodological work was made possible by grants from the Italian Telethon (B14) and the Associazione Italiana Sclerosi Multipla (AISM) to GGC and CNR target project on biotechnology to AC.


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Computation of Efficiency Index (E.I.) and Selectivity Index (S.I.).

    A modal value was computed from smooth lines fit to histograms of number of simulated PCR products per primer (see, e.g. red lines in figures 1A and 2A). The efficiency index, E.I., for each primer was computed as the decimal logarithm of the ratio:

(number of simulated PCR products for this primer)
(modal value for all the primers tested).
    The total number of coding and noncoding (3’ untranslated) base-pairs in the nonredundant pseudo-cDNA database were counted and the ratio (total coding)/(total UTR) was computed. For each primer, the simulated PCR products were grouped as "CDS" or "3’-UTR". The selectivity index, S.I., was computed for each primer as the ratio:
S.I. =    (CDS products) / (UTR products)
          (total coding) / (total UTR).

Computation of the expected distribution of PCR products per primer

    Let the databank, D, be a set of N sequences, . Given that Ss is a sequence composed of as C/G nucleotides and bs A/T nucleotides, the probability of a G or C nucleotide in the primer matching an arbitrary nucleotide in the sequence is , and the corresponding probability for A or T is  .

    In order to obtain hybridization a certain degree of matching must be obtained; here we arbitrarily decided that hybridization would occur for at least 9 matching bases out of 12, with no mismatches within the last 4 bases at the 3' end. Under these conditions, the probability of hybridization for a given template sequence and a given primer is a function of  the fraction of C/G nucleotides in the sequence, , the number of C/G in the first 8 bases of the primer, n1, and the number of C/G in the last 4 bases at the 3' end, n2.

    For any specific alignment of the primer on the template Ss, we have:

so that the probability of hybridization for any specific alignment of the primer on the template is Ps = As x Bs. The average value of Fs was 0.53 (* 0.082) and in general Ps was about 1-2x10-4, its value increasing for primers with increasing numbers of C/G nucleotides in the last 4 positions.

    Assuming that PCR products of interest would have a length, L, comprized between L0 = 100 and L1 = 1000 BP, then the number of combinations of two acceptable positions on a template sequence Ss, of length Ms is:


    This gives rise to a binomial distribution of the number of PCR products obtained from template sequence Ss of length Ms and a primer with given values of n1 and n2. Such distribution is defined by the binomial parameters   and n = Cs; the corresponding probability density function (p.d.f.) is: .

    Actually, to estimate the probability of obtaining simulated PCR products (neglecting the technical aspects connected to experimentally obtaining a PCR amplification product), the unwanted possibility of a further hybridization in between the two valid positions must be excluded. For a product of length L, this possibility has an approximate probability of , and therefore about 900 x Ps for the average product length of 450 BP. For the usual magnitude of Ps this factor amounts to about 10-2 and can be neglected.
The distributions of PCR products from the N sequences in the database   are expected to be independent. Therefore, the corresponding characteristic functions (ch.f.) can be computed   and the ch.f. for the whole databank will simply be: .

    From jD(u) the expected p.d.f. of the number of PCR products from the whole databank, pD(x), is computed for each primer. Averaging over the set of primers yields the expected distribution of the number of PCR products per primer (P1).  Notice that pD(x) is necessarily equal for primers having the same values of n1, n2 and Ps. Thus, P1 may be multimodal (up to 5 peaks for n2 = 0 to 4).

    The same procedure is used to compute the expected p.d.f. of the number of PCR products from each sequence, P2 (in this case the ch.f. is computed by summing the logs of the single ch.f.'s over the set of primers for the same sequence).

    A third distribution of interest is that of the number of "successful" primers per sequence (i.e. yielding at least one PCR product from the sequence),  P3. This is computed in the same way using the modified p.d.f., ps, such that:  .
    Distribution P1 is used to check whether the observed distribution of PCR products per primer significantly departs from the expectation: if a marked excess of particularly "good" and "poor" primers are found, this argues against a purely random distribution of nucleotides in the sequences of the databank.
Distributions P2 and P3 yield information on the exhaustivity of the approach, i.e. the capability of picking out as many different sequences as possible. In particular, the shape of the p.d.f. P3 can be compared to the corresponding distribution, obtained by the simulation experiments, to check whether any bias is present towards a subpopulation of sequences (i.e. whether some sequences are significantly more subject to amplification than others).

    This approach cannot be straightforwardly applied to the distributions obtained using sets of particularly efficient primers. These distributions are obviously shifted to the right, with respect to the p.d.f. P3, which is computed based on a purely random nucleotide composition of the databank. The size of the shift is conveniently represented by the ratio of the mean values. If the shift simply reflects an increased hybridization probability with no bias towards sequence subpopulations, the shape of the curve will be easily reproduced by computing the logarithm of the characteristic function of the expected probability, multiplying it by the ratio of the means and computing the resulting probability distribution (this is performed by applying the direct and inverse fast Fourier transforms). A reasonable agreement with the observed distribution will argue against biases in favor of specific sequence subpopulations.


Figure 1. (A) Histogram of the number of simulated CDS-containing PCR products per primer (503 primers tested on a human nonredundant cDNA database). Also shown is the expected distribution of product numbers per primer against a randomly scrambled sequence database (blue line). Notice the large excess of poorly efficient and highly efficient primers. (B) Scatter plot of the number of simulated PCR products in CDS, yielded by each primer when tested on the human (x-axis) or mouse (y-axis) cDNA databases. (C) Analysis of exhaustivity and redundancy on the results of simulated PCR (96 "best" primers - see text - tested on a human nonredundant cDNA database). Shown is the distribution of the number of simulated PCR products per transcript. The solid line represents the distribution of product numbers per transcript expected against a randomly scrambled sequence database. The dashed line represents the distribution expected after increasing the theoretical probability of matching by a factor equal to the ratio of observed to expected mean product numbers per transcript.

Figure 2. Efficiency and selectivity of pairs of dodecanucleotide primers containing a partially degenerate nucleotide at the 3' end (W or S), tested against a human nonredundant cDNA database. (A) histogram of the number of simulated PCR products per primer pair (solid line: 522 primer pairs; dashed line: 96 best pairs). (B) scatter plot of the selectivity index (SI) versus the efficiency Index (EI). See text and appendix for the meaning and computation of the two indices. The area enclosed in the square corresponds to EI's between 0.3 and 1.18 (i.e. 2 to 15 times the modal number of products) and SI's above 1.4. Primer pairs falling in this range were included in the optimal primer set, and ordered according to their SI's. The resulting primer set is reported in table 1. (C) distribution of the number of different degenerate primers yielding simulated PCR products from each transcript. Solid and dashed lines are the expected distributions before and after correcting the theoretical probability of matching as in figure 1C.

Figure 3. Relationship between redundancy (average number of simulated PCR products per transcript) and coverage (percentage of transcripts targeted by at least one primer). Simulations performed on human (Hu) and mouse (Mo) nonredundant sequence databases. All simulations  with 12-nt primers; 3 mismatches allowed, unless otherwise specified. Squares: observed coverage vs. redundancy in various simulations. (A,B) Hu, degenerate primers (max. 2 mismatches, 8 C's or G's), best 96 and all primers, respectively; (C) Mo, nondegenerate primers (6 C's or G's), 57 primers yielding >100 products; (D) Mo, nondegenerate primers (8 C's or G's), 93 primers yielding >100 products; (E) Hu, nondegenerate primers (6 C's or G's), 68 primers yielding >100 products; (F,G) Hu, nondegenerate primers (8 C's or G's), 96 best primers, and all primers, respectively; (H,I) Hu, degenerate primers (8 C's or G's), 96 best and all primers, respectively. Triangles: corresponding expected coverage, calculated for scrambled sequence databases; the observed numbers of failures are lower than expected in simulations performed with sets of selected primers (filled symbols). The dashed line represents the predictions of Poisson statistics. The continuous line is an arbitrary analytical function which suggests the following empirical relationship: coverage = 100 ´ (redundancy – 0.5) / (redundancy + 0.5) %.

Figure 4. (A) Diagram illustrating the mode of annealing of twelve-mer primers to known sequences deposited in nucleotide databases (GenBank, DBEST). Shown, is the percentage of perfect matches, as opposed to degenerate annealing, observed in 29 cases employing 8 different primers. y axis: percentages of nondegenerate annealing measured at each residue of the 29 primers analyzed. (B) Correlation between product numbers predicted by simulations and numbers of bands observed in RNA fingerprinting experiments performed with the corresponding primers. Simulations were performed on mouse nonredundant cDNA database, using 12-nt primers (8 C-G, 4 A-T), degenerate and nondegenerate. Thirteen primers were arbitrarily chosen among those yielding low, medium and high numbers of simulated PCR products; PCR experiments were performed as described in the Methods section, and only clearly discernible bands were recorded. Examples of RNA fingerprinting gels obtained with our method are published elsewhere (Malgaretti et al., 1997; Cabibbo et al., 1998)


Table 1- 96 primers selected for their high efficiency in yielding large number of PCR products, expressed as efficiency index (E.I.), and for their selectivity for coding regions versus untranslated regions of transcripts, expressed as selectivity index (S.I.). See text and Appendix for the significance and computation of the two indices.

Table 2 - Transcript sizes (kb) and coding sequence (CDS) sizes (bp) of cDNAs deposited into the Genbank database, identified by PCR-based differential screening using our computer-assisted gene fishing approach.

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