Elsevier

Gene

Volume 208, Issue 2, 22 February 1998, Pages 103-115
Gene

Improved differential screening approach to analyse transcriptional variations in organized cDNA libraries

https://doi.org/10.1016/S0378-1119(97)00658-6Get rights and content

Abstract

A cDNA library was generated from rat brain tissues and organized into 1536-well plates, using a fluorescence activated cell sorter (FACS), acting as a single cell deposition system. The organized library containing 10 000 clones, with 60% full-length cDNA inserts, allowed the generation of multiple identical membrane replicas. Each replica was hybridized with a complex probe obtained from a particular brain tissue or a given cultured cell. The signal intensity for each of the clones present on the membrane, quantified with a standard image-analysis software, is proportional both to the abundance of the corresponding mRNA in the probe and to the amount of plasmid template on the membrane. The latter value was thus used to normalize the signals produced with complex probes, to optimize the comparison of mRNA expression levels for the different systems under study. The construction of high-quality cDNA libraries, the generation of identical membrane replicas and comparable probes, and the utilization of an image-analysis software package, coupled with the normalization of the spot intensity by assaying plasmid quantity, significantly improves the differential screening approach. Altogether, these technical improvements open the possibility to compare a great number of different probes and, in consequence, to accumulate biological information for each clone present in an organized cDNA library. The functional information obtained should complement data from DNA sequencing projects.

Introduction

In recent years, numerous genome sequencing projects and systematic analysis of cDNA libraries (Adams et al., 1991, Adams et al., 1992, Adams et al., 1995) have led to the identification of an increasing number of new gene sequences. However, these approaches do not usually permit functional characterization of the genes.

The temporal, developmental, topographical and physiological patterns in which a gene is expressed provide clues to its biological role (Schena et al., 1995). Hence, it seems possible to obtain hints on functional information about genes by identifying those which are differentially expressed under distinct biological conditions (Calvet, 1991). The differences in gene expression may be measured by analysing the corresponding variations in mRNA expression levels.

Several experimental approaches can be used to identify genes based on their expression pattern: differential PCR display (Liang and Pardee, 1992; Wan et al., 1996); subtractive libraries (Sargent, 1987; Nedevi et al., 1993), suppression subtractive hybridization (Diatchenko et al., 1996), serial analysis of gene expression (Velculescu et al., 1995) and differential screening on organized cDNA libraries (Okubo et al., 1992; Zhao et al., 1995; Takahashi et al., 1995; Nguyen et al., 1995). The techniques based on PCR, such as differential PCR display, are potentially the fastest methods for identifying differentially expressed genes, using relatively small amounts of mRNA and without the necessity for constructing cDNA libraries. However, these methods produce a high level of false positives and artifactual responses (Sompayrac et al., 1995; Bertioli et al., 1995).

Despite the successful identification of numerous important genes using subtraction techniques, these methods require a great amount of poly A+ RNA. In addition, they involve a high number of controls and often, multiple subtraction steps, which render reproducibility nearly impossible.

Among the nucleic acid techniques, the hybridization of arrayed cDNA libraries by complex probes enables one to visualize the expression level of many thousands of genes corresponding to a given biological state. Therefore, differential screening analysis permits the comparison of several biological conditions and the identification of transcripts which show significant variations, thus allowing for the accumulation of biological information for the whole set of clones present in the arrayed library.

The success of the differential screening approach mainly depends on: (1) the quality and quantity of clones present in the cDNA reference library; (2) the possibility to rapidly organize, replicate and store a large number of clones; (3) the use of complex probes with similar cDNA patterns, capable of detecting weakly expressed genes; (4) the availability of an analytical framework to quantitatively correlate information resulting from the hybridization of the library with different probes.

We present here a strategy that fulfils most of the abovementioned conditions. We have constructed a cDNA library from mRNA extracted from different rat brain tissues. The library contained approx. 10 000 clones, with a low number of redundancies and approx. 60% of full-length cDNA sequences. It was organized into 1536-well dishes, using a fluorescence activated cell sorter (FACS) acting as a single cell deposition system (Magazin et al., 1992). High density colony filters were prepared using a modified BIOMEK 1000 workstation. The identical replicates were screened with different probes capable of detecting weakly expressed genes. The probes were specially prepared to have similar cDNA size profiles and the same specific activity.

We also show how a standard software package (Visage 2D Investigator Database of BioImage) can be adapted to analyse digital images corresponding to the hybridization of the filters with different probes. In addition, we propose a normalization method, based on the available quantity of plasmid material on the filters, that greatly improves the performance of the differential screening approach.

Altogether, the above technical improvements open the possibility to compare a great number of different probes and, in consequence, to accumulate biological information for each clone present in an organized cDNA library.

Section snippets

Construction of a cDNA reference library

60 male, 8–10-week-old Sprague–Dawley rats were used; brains were dissected for the isolation of cortex, septum, striatum and hippocampus and stored at −80°C. RNA was extracted from the isolated tissues by the acid phenol/guanidine thiocyanate method of Chomczynski and Sacchi (1987). RNA poly A+ was prepared from rat brain using oligo (dT)-magnetic beads (Dynal) and quantified using 3H-poly(U). mRNAs were pooled and used for the preparation of cDNA using SuperScript II reverse transcriptase

Quality of the reference library

Successful differential screening depends on the quality and quantity of clones present in the reference library. In our case, the total content of the library was approx. 106 clones. A fraction of them was used to obtain a cDNA library array containing approx. 104 clones (ten plates of 1536 wells), following the above described experimental strategy (Fig. 1).

The quality of the reference library can be extrapolated from the analysis of 298 cDNA clones that were selected as described in Section

Discussion

Systematic sequencing of human cDNA libraries is generating lists of genes expressed in many different tissues (Adams et al., 1995). It is difficult and time-consuming to determine the biological function of a gene merely from knowledge of its sequence. However, useful functional information may be obtained by identifying gene expression variations in cells or tissues under different biological conditions. Therefore, the use of the differential screening approach to analyse transcriptional

Acknowledgements

We thank D. Shire and M. Magazin for valuable comments and corrections to the manuscript.

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