Faculty | Ecology & Evolution | University of Chicago

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Faculty : Students : Administrative Staff : Research Staff

Ilya Ruvinsky, Ph.D.
Assistant Professor
Department of Ecology & Evolution
Department of Organismal Biology and Anatomy
Committee on Genetics, Genomics & Systems Biology
Committee on Developmental Biology
Committee on Evolutionary Biology

Office: Erman 304 | Phone: 773-702-1533 | Fax: 773-702-9740 | email:ruvinsky(at)uchicago(dot)edu
Subjects: Evolution of development, particularly the evolution of transcriptional regulation (using C. elegans as a primary model organism); Comparative and computational genomics; Molecular evolution

Ruvinsky Lab

Research Interests

My laboratory is broadly interested in the evolution of development (Evo-Devo), evolutionary genomics and molecular evolution. We integrate developmental, genomic and computational approaches to understand the evolution of genes and gene functions. Students and post-docs are encouraged to develop their projects under the broad umbrella of these research interests.

The current view of developmental evolution posits that morphological differences between species are often caused by changes in regulatory (as opposed to coding) DNA sequences. Despite the importance of these cis-elements for gene regulation, much remains to be learned about their evolution. We are working to fill this gap.

Orthologous genes are often expressed in similar patterns even between distantly related species. Coupled with a high degree of functional conservation of transcription factors, this would suggest that cis-regulatory elements have also been conserved over long periods of time. However, this does not appear to be the case when the cis-regulatory elements of Drosophila genes are tested in C. elegans (Ruvinsky and Ruvkun 2003). Promoter swaps between closely related species of nematodes show that even over much shorter phylogenetic distances there is a noticeable amount of functional divergence.

A possible explanation for this paradox could be that promoters co-evolve with the transcription factors that mind them and this results in the conservation of gene expression patterns despite rapid sequence turnover. To test this hypothesis, we are currently dissecting the mechanism(s) responsible for the conservation of expression of the unc-47 gene between C. elegans and a closely related species C. briggsae (Barrière and Ruvinsky, in preparation).

In parallel we are testing the functions in C. elegans of numerous orthologous regulatory elements from a variety of related nematodes (Barrière et al., in preparation). Our goal is to elucidate the “tempo and mode” of cis-regulatory evolution.

Recent Publications

Barrière A., Yang S.-P., Pekarek E., Thomas C. G., Haag E. S. and Ruvinsky I. (2009). Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 19: 470-480.

Ruvinsky I., Ohler U., Burge C. B. and Ruvkun G. (2007). Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302: 617-626.

Ruvinsky I. and Ruvkun G. (2003). Functional tests of enhancer conservation between distantly related species. Development 130: 5133-5142.

Ruvinsky I. and Gibson-Brown J. J. (2000). Genetic and developmental bases of serial homology in vertebrate limb evolution. Development 127: 5233-5244.

Ruvinsky I., Silver L. M. and Gibson-Brown J. J. (2000). Phylogenetic analysis of T-box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. Genetics 156: 1249-1257.