Gene expression patterns in development

Read Also

Embryonic development encompasses the complete spectrum of developmental and cell biological processes and thus it is not surprising that we failed to detect the expression of only 20% of genes in the embryo. This is an overestimate of the number of genes not expressed during embryogenesis, since we have indication from microarray data that some late embryonic genes escaped detection in our in situ assay because they are not expressed until after deposition of the cuticle prevents the use of the in situ method. On the other hand for genes that are expressed in a very small subset of embryonic cells the in situ assay is more sensitive than microarray analysis (data not shown).

45% of genes in our unbiased set are expressed in broad patterns. Broad genes tend to encode proteins that mediate core cellular processes and their apparent patterns reflect quantitative differences in requirements for basic cellular machineries in different tissues, especially late in embryogenesis.

35% of genes in our dataset show spatially and/or temporally restricted gene expression. Our data reveal a tremendous diversity of gene expression patterns. Sets of genes that exhibit exactly the same tissue specific gene expression are rare, small and usually limited to mature organs. Genes with identical expression patterns that span across multiple stages of embryogenesis were not found, even at the limited resolution level offered by our imaging technique. Genes that are expressed during mid-embryogenesis in a specific tissue very frequently show unrelated patterns earlier and later in development. Consequently genes that serve as lineage markers by being expressed in a given organ system from anlagen, through primordia to final differentiated organs are rare and, for the most part, had already been discovered by genetic analysis.

In order to detect regularity and impose classification on the complex expression pattern space we had to resort to a fuzzy clustering approach which allows a gene with a complex expression pattern to participate in multiple clusters. We found that nearly all genes with restricted patterns fell into one of six clearly distinguishable restricted pattern types: (1) yolk, blood and fat; (2) epidermus; (3) nervous system; (4) muscle; (5) blastoderm; and (6) several smaller organ specific patterns. Within each of these basic types, several subtypes were distinguished by their preferential expression in particular combinations of tissues.

Remarkably 41% of the genes belong to more than one cluster underscoring the overall gene expression pattern diversity. It is perhaps expected that majority of patterns will be unique when one looks at the pattern across all developmental stages. The biology of early and late Drosophila embryo is very different and the diversity of patterns suggests that many genes are turned on independently multiple times in development. It is less intuitive, that even when one looks exclusively at spatial pattern at the late stages of embryogenesis, that individual genes are expressed in almost all combinations of organ systems. The existence of expression clusters indicates that restriction of gene activities to organ systems and developmental lineages frequently occurs, whereas the fuzziness of the clusters suggests that, at least for some genes, expression in atypical combinations of tissues can be achieved.  It will be interesting to investigate the cis-regulatory code that leads to this regularity of recurring patterns and the tremendous potential for diversity in gene expression regulation for individual genes. Since gene expression regulation in the best studied setting of segmentation gene network is thought to be modular, it is possible that the overall diversity of patterns is achieved by a combination of a significantly smaller number of regulatory modules.

What is the functional significance of the observed pattern diversity? Are all the minute features of the vast number of unique patterns necessary to carry out development? Or is the complexity of patterns largely a spurious consequence of position effects in the proximity of regulatory modules that have little deleterious effect. Drosophila is very well positioned to address these questions, since 12 complete genomes have been recently sequenced and RNA in situ hybridization is applicable in each of them. Careful comparisons of gene expression patterns across multiple closely related species should reveal the patterns that are under evolutionary constraint. Our genome-wide dataset of patterns in Drosophila melanogaster serves as a starting point for further investigation of genomic regulatory networks in development and their evolution.

---