Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions
Article first published online: 17 APR 2012
© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust
Volume 195, Issue 1, pages 248–263, July 2012
How to Cite
Zhang, L. and Ma, H. (2012), Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions. New Phytologist, 195: 248–263. doi: 10.1111/j.1469-8137.2012.04143.x
- Issue published online: 24 MAY 2012
- Article first published online: 17 APR 2012
- Received: 13 January 2012, Accepted: 6 March 2012
- animals and plants;
- gene duplication;
- lysine methylation;
- SET domain genes
- •Plants and animals possess very different developmental processes, yet share conserved epigenetic regulatory mechanisms, such as histone modifications. One of the most important forms of histone modification is methylation on lysine residues of the tails, carried out by members of the SET protein family, which are widespread in eukaryotes.
- •We analyzed molecular evolution by comparative genomics and phylogenetics of the SET genes from plant and animal genomes, grouping SET genes into several subfamilies and uncovering numerous gene duplications, particularly in the Suv, Ash, Trx and E(z) subfamilies.
- •Domain organizations differ between different subfamilies and between plant and animal SET proteins in some subfamilies, and support the grouping of SET genes into seven main subfamilies, suggesting that SET proteins have acquired distinctive regulatory interactions during evolution. We detected evidence for independent evolution of domain organization in different lineages, including recruitment of new domains following some duplications.
- •More recent duplications in both vertebrates and land plants are probably the result of whole-genome or segmental duplications. The evolution of the SET gene family shows that gene duplications caused by segmental duplications and other mechanisms have probably contributed to the complexity of epigenetic regulation, providing insights into the evolution of the regulation of chromatin structure.