Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

Patterning of C. elegans vulval cell fates relies on inductive signaling. In this induction event, a single cell, the gonadal anchor cell, secretes LIN-3/EGF and induces three out of six competent precursor cells to acquire a vulval fate. We previously showed that this developmental system is robust to a four-fold variation in lin-3/EGF genetic dose. Here using single-molecule FISH, we find that the mean level of expression of lin-3 in the anchor cell is remarkably conserved. No change in lin-3 expression level could be detected among C. elegans wild isolates and only a low level of change-less than 30%-in the Caenorhabditis genus and in Oscheius tipulae. In C. elegans, lin-3 expression in the anchor cell is known to require three transcription factor binding sites, specifically two E-boxes and a nuclear-hormone-receptor (NHR) binding site. Mutation of any of these three elements in C. elegans results in a dramatic decrease in lin-3 expression. Yet only a single E-box is found in the Drosophilae supergroup of Caenorhabditis species, including C. angaria, while the NHR-binding site likely only evolved at the base of the Elegans group. We find that a transgene from C. angaria bearing a single E-box is sufficient for normal expression in C. elegans. Even a short 58 bp cis-regulatory fragment from C. angaria with this single E-box is able to replace the three transcription factor binding sites at the endogenous C. elegans lin-3 locus, resulting in the wild-type expression level. Thus, regulatory evolution occurring in cis within a 58 bp lin-3 fragment, results in a strict requirement for the NHR binding site and a second E-box in C. elegans. This single-cell, single-molecule, quantitative and functional evo-devo study demonstrates that conserved expression levels can hide extensive change in cis-regulatory site requirements and highlights the evolution of new cis-regulatory elements required for cell-specific gene expression

From phrase structure to dependencies, and back

Transforming constituent-based annotation into dependency-based annotation has been shown to work for different treebanks and annotation schemes (e.g. Lin (1995) has transformed the Penn treebank, and Kübler and Telljohann (2002) the Tübinger Baumbank des Deutschen (TüBa-D/Z)). These ventures are usually triggered by the conflict between theory-neutral annotation, that targets most needs of a wider audience, and theory-specific annotation, that provides more fine-grained information for a smaller audience. As a compromise, it has been pointed out that treebanks can be designed to support more than one theory from the start (Nivre, 2003). We argue that information can also be added to an existing annotation scheme so that it supports additional theory-specific annotations. We also argue that such a transformation is useful for improving and extending the original annotation scheme with respect to both ambiguous annotation and annotation errors. We show this by analysing problems that arise when generating dependency information from the constituent-based TüBa-D/Z