Functional tests of enhancer conservation between distantly related species

Abstract

Expression patterns of orthologous genes are often conserved, even between distantly related organisms, suggesting that once established, developmental programs can be stably maintained over long periods of evolutionary time. Because many orthologous transcription factors are also functionally conserved, one possible model to account for homologous gene expression patterns, is conservation of specific binding sites within cis-regulatory elements of orthologous genes. If this model is correct, a cis-regulatory element from one organism would be expected to function in a distantly related organism. To test this hypothesis, we fused the green fluorescent protein gene to neuronal and muscular enhancer elements from a variety of Drosophila melanogaster genes, and tested whether these would activate expression in the homologous cell types in Caenorhabditis elegans. Regulatory elements from several genes directed appropriate expression in homologous tissue types, suggesting conservation of regulatory sites. However, enhancers of most Drosophila genes tested were not properly recognized in C. elegans, implying that over this evolutionary distance enough changes occurred in cis-regulatory sequences and/or transcription factors to prevent proper recognition of heterospecific enhancers. Comparisons of enhancer elements of orthologous genes between C. elegans and C. briggsae revealed extensive conservation, as well as specific instances of functional divergence. Our results indicate that functional changes in cis-regulatory sequences accumulate on timescales much shorter than the divergence of arthropods and nematodes, and that mechanisms other than conservation of individual binding sites within enhancer elements are responsible for the conservation of expression patterns of homologous genes between distantly related species.

A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans

“…By testing the expression pattern of enhancers from Drosophila in C. elegans, it has been shown that changes in cis-regulatory sequences accumulate relatively fast, while expression patterns remain conserved along animal evolution (Ruvinsky and Ruvkun 2003). This may explain why the motif pair was observed here only in the Caenorhabditis genus.…”

The frailty of adaptive hypotheses for the origins of organismal complexity

“…Thus, the new regulatory architecture emerges beneath a constant phenotype, without any bottleneck in fitness during the transitional phase of mixed genotypes. Such neutral transitions may help explain apparent cases of ''developmental system drift,'' whereby closely related species achieved similar morphological structures by substantially different mechanisms (59,63,(71)(72)(73)(74).…”

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

“…Although many of the key enzymes responsible for deposition and maintenance of H3K27me3 are known, it is likely that we do not have a complete catalog of all the elements of all PREs (Delest et al 2012), nor do we know the exact spatial or orientation requirements of the involved binding sites (if indeed there are any). However, the extreme conservation of H3K27me3 across distantly related species leads to the question of how a cis-regulatory element composed of relatively degenerate sequence motifs could persist functionally over such a long period of time (Ruvinsky and Ruvkun 2003;Fisher et al 2006).…”