Differential colony hybridization: molecular cloning from a zero data base

Hunting for differentially expressed genes

Differentially expressed genes are usually identified by comparing steady-state mRNA concentrations. Several methods have been used for this purpose, including differential hybridization, cDNA subtraction, differential display and, more recently, DNA chips. Subtractive hybridization has significantly improved after the polymerase chain reaction was incorporated into the original method and many new protocols have been established. Recently, the availability of the wellknown coding sequences for some organisms has greatly facilitated gene expression analysis using high-density microarrays. Here, we describe some of these modifications and discuss the benefits and drawbacks of the various methods corresponding to the main advances in this field.

Cloning and characterization of cDNAs from genes differentially expressed during the strawberry fruit ripening process by a MAST-PCR-SBDS method

A vast number of clones carrying cDNAs from genes differentially expressed along the strawberry (Fragaria x ananassa c.v. Chandler) fruit ripening process has been isolated by screening of a subtractive cDNA library. The library was constructed and screened using a powerful procedure that combines the differential screening technique with a Southern blot screening by means of the polymerase chain reaction (PCR-SBDS procedure). Several clones have been partially sequenced and characterized and main similarities with other known genes from higher plants are presented. These comparisons reveal putative functions of these genes in the strawberry fruit ripening process.

Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo

A total of 5 conventional, directionally cloned plasmid cDNA libraries have been constructed from the entire embryonic region of the mid-gastrulation mouse embryo and from its four principal tissue constituents (ectoderm, mesoderm, endoderm and primitive streak). These libraries have been validated with respect to the number of independent clones, insert-size and appropriate representation of diagnostic marker genes. Subtractive hybridisation has been used to remove clones common to the Endoderm and Mesoderm cDNA libraries resulting in an Endoderm minus Mesoderm subtracted library. Probe prepared from this subtracted library has been hybridised to a grid containing approximately 18,500 Embryonic Region library clones. Three novel clones have been recovered as well as expected genes already known to be highly expressed in the primitive endoderm lineage at this stage of development. In situ hybridisation to early postimplantation embryos has revealed the expression patterns of these novel genes. One is highly expressed exclusively in visceral endoderm, one is expressed in ectodermal and endodermal tissues, and the third proves to be an early marker of prospective and differentiated surface ectoderm as well as being expressed in endoderm and its derivatives.

Protein analysis on a genomic scale

Methods for protein analysis, such as chromatography, electrophoresis, enzyme tests, receptor assays and immunological tests, have always been aimed in a classical reductionistic manner at investigating single proteins isolated from the complex protein composition of biological compartments. The complexity of the protein composition in biological systems was first visualized by two-dimensional electrophoresis (2-DE). Using 2-DE like a molecular microscope, protein variations between different biological situations may be detected by subtractive 2-DE analyses. Combining 2-DE with microsequencing, amino acid analysis and mass spectrometry protein spots on 2-DE gels may be identified. The sequence information can be used to find the gene. However, by 2-DE not only single protein changes can be detected and investigated on the gene level, but also complex changes of many proteins on a genomic scale.

In search of cytokine-response genes

The development of efficient cloning methods for the isolation of cytokine-response genes is vital to our understanding of how cytokines elicit distinct cellular responses. Here, Carol Beadling and Kendall Smith describe a straightforward and rapid method that has been used to clone interleukin 2 (IL-2)-induced genes.

Strategies for identification of peptide growth factors

Numerous peptides are known that have specific functions as growth factors in different tissues. These bioactive peptides are characterized by their ability to bind to high-affinity receptors, by their classification into superfamilies that share homology and function and by their synthesis as large precursor molecules that are processed to active forms. In some cases the precursors themselves also have biological activity. Modulation of growth factor activity at the level of the receptor or effector molecules has great therapeutic potential. This article will outline some of the strategies that have been successful in detecting and identifying growth factors and demonstrating their biological activity.

An estimation of the sensitivity of in vitro translation using two-dimensional gel analysis

Poly (A+ mRNA species, isolated from 100-day-old rat brain, were analysed by in vitro translation and two-dimensional gel electrophoresis. The synthesis of selected protein species was compared to actin on the basis of [35S]methionine incorporation. The estimated molar abundance of translation products varied from abundant species at 0.78% of the total to several are species, detectable below the 0.02% level. If these synthesis rates reflect the abundance of particular mRNAs in the mixture, this sensitivity limit compares well with accepted values using differential cDNA screening techniques. This analysis provides evidence that in vitro translation methodology is able to detect rarer mRNA species than is usually expected--these include similar abundance classes to library screening procedures.

Study of transcription in measles virus-infected Vero cells using cDNA probes prepared from poly(A)RNA from uninfected and infected cells

From af primary plasmid cDNA library prepared from measles virus-infected Vero cell poly(A)RNA, 435 clones selected at random were used to examine the sensitivity and specificity of cDNA probes derived from total poly(A)RNA from uninfected and infected Vero cells. The correlation between the abundance level of a particular species in the cDNA probe and the hybridization signal strength generated by the corresponding cDNA clone on a filter was reliably determined only when at least three independently prepared filters were examined. Variation in the amount of target plasmid was the most important cause of spurious signals. Variation in cDNA insert length did not disturb the signal strength within certain limits. cDNA species with abundance levels down to 0.08-0.01% were able to produce a hybridization signal above background. Unspecific cross-hybridization was shown to define the sensitivity limit of mixed cDNA probes. Despite the many false signals present at different stages, cDNA probes provided valuable information: the cDNA probes were used to monitor relative RNA expression levels and to clone five different measles virus transcripts and 2 host cell transcripts more abundantly expressed in infected cells. The abundance levels of the measles virus nucleocapsid, phosphoprotein, matrix, fusion protein and haemagglutinin genes were 1.5%, 1.5%, 1%, 0.75% and 0.5%, respectively, of the total cDNA library.

Isolation of immediate-early differentiation mRNAs by enzymatic amplification of subtracted cDNA from human endothelial cells

The phenomena of cell growth and differentiation result from unique transcriptional programs. Inducible genes are therefore differentially expressed in response to various biochemical stimuli that regulate cell division and differentiation. To isolate differentially expressed mRNAs of unknown sequence, two techniques, differential and subtractive hybridization, have been used. Subtractive hybridization is superior for the isolation of rare mRNAs; however, its utility is somewhat limited by the fact that large amounts of driver mRNA are required for the procedure. We have used the polymerase chain reaction (PCR) to amplify minute quantities of unknown subtracted sequences, and thus, enhanced the sensitivity and ease of cloning differentially expressed mRNAs. We demonstrate the utility of this technique by describing the isolation of at least four unique cDNA clones of human endothelial cell mRNAs that are induced by the tumor promoter, phorbol ester, a factor that promotes immediate early events during the endothelial cell differentiation pathway in vitro.

Frontiers in mammalian cell culture

For the past 60 years, fundamental discoveries in eukaryotic biology using mammalian cell cultures have been significant but modest relative to the enormous potential. Combined with advances in technologies of cell and molecular biology, mammalian cell culture technology is becoming a major, if not essential tool, for fundamental discovery in eukaryotic biology. Reconstruction of the milieu for cells has progressed from simple salt solutions supporting brief survival of tissues outside the body to synthesis of the complete set of structurally defined nutrients, hormones and elements of the extracellular matrix needed to reconstruct complex tissues from cells. The isolation of specific cell types in completely defined environments reveals the true complexity of the mammalian cell and its environment as a dynamic interactive physiological unit. Cell cultures provide the tool for detection and dissection of the mechanism of action of cellular regulators and the genes that determine individual aspects of cell behavior. The technology underpins advances in virology, somatic cell genetics, endocrinology, carcinogenesis, toxicology, pharmacology, hematopoiesis and immunology, and is becoming a major tool in developmental biology, complex tissue physiology and production of unique mammalian cell-derived biologicals in industry.

Isolation of cDNAs of scrapie-modulated RNAs by subtractive hybridization of a cDNA library

We have developed a subtractive cloning procedure based on the hybridization of single-stranded cDNA libraries constructed in pi H3M, a vector containing the phage M13 origin of replication. We have used this strategy to isolate three transcripts whose abundance is increased in scrapie-infected brain. DNA sequence analysis showed that they represent glial fibrillary acidic protein, metallothionein II, and the B chain of alpha-crystallin; the latter two may represent a response to stress.