Title:
Evolution of cis-regulatory elements and genetic networks after genome duplication

Hajime Ogino, Ph.D.
Research team leader
Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
8916-5, Takayama, Ikoma, Nara , 630-0192, Japan

Abstract:
 During chordate evolution, whole-genome duplications (WGDs) generated a number of duplicated gene pairs (known as paralogs) from the ancestral gene set, with members of sibling paralog pairs often showing overlapping, yet distinct, expression patterns in modern vertebrates. Although the diversification of paralog expression is thought to have made a significant contribution to the development of complex genetic networks, little is known about how the cis-regulation of such paralogs has changed, or how novel genetic networks have emerged as a consequence (1). To address these issues, we analyzed regulation of the vertebrate paralogs, pax2 , pax5 and pax8 , and regulation of their single amphioxus ortholog, pax2/5/8 . The vertebrate pax2 , pax5 and pax8encode paired-domain transcription factors and play essential roles in eye, ear, brain, and kidney development, and their amphioxus ortholog is expected to retain the ancetral, pre-WGD mode of the cis-regulation (2, 3).
Our genome-wide enhancer screening using a high-throughput transgenesis method in Xenopusrevealed that pax2 , pax5 and pax8 retain enhancers which appear to be derived from their common progenitor gene (4). These ancestral-type enhancers are capable of driving pax2 -like, multi-tissue expression in the eye, ear, brain and kideny, despite that expression of pax5 and pax8localizes to a subset of pax2 -expressing tissues, such as the brain and kideny. Further analysis of the pax2 and pax8 cis-regulation and comparison with cis-regulation of the amphioxus pax2/5/8showed that the divergence in pax2 and pax8 expression was generated by innovation of a tissue-specific silencer in pax8 after the WGD. Regarding pax5 , we found that anitisense knockdown ofpax2 releases the suppression of its ancestral-type enhancer in the pronephros, and activates the endogenous pax5 expression to partially compensate the pax2 function. These results suggest that modern vertebrates are still using the ancestral mode of gene regulation as a ground state, which was modified by silencer innovation for the diversification of paralog expression, and re-wired for the innovation of a fail-safe system that provides robustness to the organ formation.

References:
(1) Postlethwait, J., Amores, A., Cresko, W., Singer, A. & Yan, Y. L.: Subfunction partitioning, the teleost radiation and the annotation of the human genome. Trends Genet. 20, 481-490 (2004).

(2) Goode, D. K. & Elgar, G.: The PAX258 gene subfamily: a comparative perspective. Dev. Dyn.238, 2951-2974 (2009).

(3) Kozmik, Z., Holland , N. D., Kalousova, A., Paces, J., Schubert, M. & Holland, L. Z . : Characterization of an amphioxus paired box gene, AmphiPax2/5/8 : developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. Development 126, 1295-1304 (1999).