Evolutionary dynamics and functional roles of regulatory systems in plants

Transcription, the process of generating RNA copies of the genetic information stored in the DNA, is crucial for every organism. As with other essential processes in life, correct activation and repression of transcription is governed by complex regulatory mechanisms. These regulatory mechanisms operate and interact at several levels, ranging from signals encoded by the DNA sequence, such as transcription factor binding sites, to higher order structures and signals at the level of chromatin, involving DNA methylation and histone modifications. Regulatory mechanisms are not inert but instead, change and evolve. While alterations in regulation often result in lower fitness, they are also important for population variation as well as large phenotypic evolutionary changes in the long run. For example, one of the main reasons why humans are different from chimpanzees lies in the differences between the regulatory regions of their genes. Thus, to understand evolution of organisms as well as their biology, understanding the evolution of regulatory mechanisms is of utmost importance. The reverse is also true: studying evolution of regulatory features in the genome sequence can aid in determining their function. In this thesis, I describe four studies on both evolution and function of plant regulatory mechanisms. I focus on chromatin-level regulation, namely on two covalent histone modifications that play important roles in developmental regulation. Chapter 2 describes the evolution of the protein complex Polycomb repressive complex 1 (PRC1) that ubiquitinates the histone H2A. This protein complex is ancient as it originated before the last eukaryotic common ancestor but has also changed it composition and contains plant-specific subunits. We show that all core subunits of the plant PRC1 were present at least in the last common ancestor of seed plants, earlier than previously thought, improving our understanding of the importance of the Polycomb proteins for plant evolution. In Chapter 3 focuses on a related regulatory complex, PRC2, that deposits the histone modification H3K27me3. We analyze the fate of H3K27me3 after gene duplication, and demonstrate that paralogs tend to retain the regulatory state of their ancestor. We also find that H3K27me3 correlates with conserved noncoding sequences (CNSs) in their upstream regions, the first time that H3K27me3 in plants has been associated to a potential genome wide regulatory signal at the DNA level. Chapter 4 analyzes the interplay between PRC1 and PRC2. The currently proposed recruitment model for the two complexes states that PRC2 is the first to be recruited to a specific locus, where it deposits H3K27me3. Subsequently, PRC1 recognizes H3K27me3 and deposits H2Aub. Based on a bioinformatics reanalysis of published data on genome-wide localization of PRC1 and PRC2, we show that the target genes of the two complexes differ in their properties and thus recruitment mechanism is likely more complex than the currently proposed model. Chapter 5 revolves around the evolutionary impact of H3K27me3. We find that paralogs covered by this modification show faster coding sequence evolution, yet slower evolution of expression patterns and upstream regulatory regions. We can thus an associate HK27me3 with distinct evolutionary fates compared to other genes. This thesis combines functional and evolutionary data to reveal the evolutionary history of a regulatory protein complex as well as analyze the properties and fate of the regulated genes. Altogether, it sheds some more light on the way plants regulate the expression of their genes, underlining the importance of integrating functional and evolutionary studies.