An analysis of expression patterns of genes encoding proteins with catalytic activities

Abstract

Background: In situ hybridization (ISH) is a powerful method for visualizing gene expression patterns at the organismal level with cellular resolution. When automated, it is capable of determining the expression of a large number of genes.

Results: The expression patterns of 662 genes that encode enzymes were determined by ISH in the mid-gestation mouse embryo, a stage that models the complexity of the adult organism. Forty-five percent of transcripts encoding metabolic enzymes (n = 297) showed a regional expression pattern. A similar percentage was found for the 190 kinases that were also analyzed. Many mRNAs encoding glycolytic and TCA cycle enzymes exhibited a characteristic expression pattern. The annotated expression patterns were deposited on the Genepaint database and are retrievable by user-defined queries including gene name and sites of expression.

Conclusion: The 662 expression patterns discussed here comprised gene products with activities associated with catalysis. Preliminary analysis of these data revealed that a significant number of genes encoding housekeeping functions such as biosynthesis and catabolism were expressed regionally, so they could be used as tissue-specific gene markers. We found no difference in tissue specificity between mRNAs encoding housekeeping functions and those encoding components of signal transduction pathways, as exemplified by the kinases.

Figure 1

Examples of tissue-specific molecular markers in the E14.5 mouse embryo. A and B. Prostaglandin D2 synthase (brain) (Ptgds) (Genepaint set ID HD33, image 2C) expression is exclusive to the meninges (me), choroid plexi (cp, A) and gonads (g, B). C. Lysyl oxidase-like 3 (Lox13) (MH1813, 4A) is exclusively expressed in cartilage (ca). D and E. Ribonuclease T2 (Rnaset2) (MH1633, 1A, 5A) is a suitable marker for lens (le, D) and choroid plexi (cp, E). F and G. Acetyl-Coenzyme A synthetase 2 (AMP forming)-like (Acas2l) (MH1439, 4C, 4B) marks the ventricular zones of the nervous system (vz, F), including that of the spinal cord (sp, G), and liver (not shown). H. The gene Carboxypeptidase N polypeptide 1 (Cpn1) (MH1654, 5B) marks liver (li), pancreas (pa) and stomach (so). I and J. Expression of Alcohol dehydrogenase 1 (class I) (Adh1) (MH1744, 3D) is seen in adrenal gland (a, I), lung mesenchyme (lu, I) and nasal epithelium (n, J). K and L. Phospholipase A2 (Pla2g2f) (MH1625, 3A) expression is restricted to the lung (lu, K) and the adrenal gland (a, L). M and N. Glucokinase (Gck) (MH1608, 4C) is exclusive to the ventromedial nucleus of the hypothalamus (vt), preoptic area, anterior pituitary (pi, M) and pancreas (pa, N), O – Q. Expression of Carbonic anhydrase 14 (Car14) (MH1292, 3C, 1A) in choroids plexi (cp, O and P) and retina (re, Q).

Figure 2

Expression pattern of Isocitrate dehydrogenase 3 (NAD+) alpha, (Idh3a), a representative example of a gene with a stereotypical energy metabolism pattern (SEMP). Idh3a (MH 965, 4C) is expressed widely in CNS, PNS, muscle, liver, kidney, lung, heart, pancreas, intestine, thymus, epithelia covering the alimentary and respiratory tract and whisker follicles. Relevant to the definition of SEMP is a relative regional elevation of expression, e.g. in the neocortex (nx), cranial ganglia (cg), dorsal root ganglia (drg), spinal cord (sc), heart (h), liver (li), lung (lu), intestine (i), salivary glands (sg) and muscles (m). Furthermore, a feature of a SEMP is the absence of expression in cartilage of the axial (ac) and appendicular skeletal anlage (not shown).

Figure 3

Matrices representing the expression pattern of glycolysis (A) and TCA cycle (B) genes in signature tissues. The expression level for each gene is shown in color. Red signifies strong expression; yellow, medium; and blank, weak expression. In cases where transcripts could not be detected, boxes are shown in blue. The Genepaint set IDs point to the data sets from which quantitative assessments were made. Genes showing a SEMP are in bold.