Evolution of microsynteny in vertebrates

Evolution of microsynteny in vertebrates

Lab members: Maria Touceda-Suárez
Funding: CRG

The order of genes along metazoan chromosomes has generally been thought to be largely random, with few implications for organismal function. However, through a multi-species genome comparison, we found hundreds of pairs of genes that have remained linked in diverse metazoan species over hundreds of millions of years of evolution, suggesting widespread functional implications for gene order. These associations appear to largely reflect cis-regulatory constraints, with either (i) multiple genes sharing transcriptional regulatory elements (Figure, top), or (ii) regulatory elements for a developmental gene being found within a neighboring 'bystander' gene (known as a Genomic Regulatory Block)(Figure, bottom). Recent techniques to map three-dimensional interactions across multiple genomic regions are completing this picture, blurring the traditional boundaries of individual genes and creating a more complex and intricate scenario defined by gene-gene interactions.


Modified from Irimia et al, Trend Genet 2013

 In this line of research, we investigate the evolutionary fate of ancient genomic regulatory blocks – originated by the last common ancestor of Bilaterians – after the two rounds of whole genome duplication occurred at the origin of vertebrates. Differential gene conservation and loss in different lineages have contributed to shape our genomes, providing explanations for striking features such as ancient vast gene deserts.

Related publications:

  • Irimia, M., Maeso, I., Tena, J.J., Roy, S.W., Fraser, H.B. (2013). Ancient cis-regulatory constraints and the evolution of genome architecture. Trends Genet, 29(9):521-8.
  • Irimia, M., Tena, J.J., Alexis, M.S., Fernandez-Miñan, A., Maeso, I., Bogdanović, O., de la Calle-Mustienes, E., Roy, S.W., Gomez-Skarmeta, J.L., Fraser, H.B. (2012). Extensive Conservation of Ancient Microsynteny across Metazoans due to cis-regulatory Constraints. Genome Res, 22(12): 22(12):2356-67.
  • Maeso, I. *, Irimia, M.*, Tena, J.J.*, González-Pérez, E.*, Tran, D., Ravi, V., Venkatesh, B., Campuzano, S., Gómez-Skarmeta, J.L., Garcia-Fernàndez, J. (2012). An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. Genome Res, 22(4):642-55.