Search

Additional file 1: Figure S1. Strategy of generating H2Aub depleted lines. Figure S2. Comparison of H3K27me3 data of this study with previously published data. Figure S3. H2Aub is essential for H3K27me3 incorporation. Figure S4. Distribution of H2Aub and H3K27me3 peaks among functional features of the Marchantia genome. Figure S5. H3K27me3 targeting is generally affected on genes in H2Aub deficient lines. Figure S6. H2Aub is required for gene repression and activation. Figure S7. Characterization of strong double mutant allele combinations in MpBMI1/1L. Figure S8. Characterization of weak double mutant allele combinations in MpBMI1/1L. Figure S9. Deposition of H2Aub is affected on upregulated and downregulated genes by loss of MpBMI1/1L. Figure S10. PRC1-mediated gene repression and activation depends on H2Aub. Figure S11. H2Aub contributes to PRC1-mediated transposable element activation. Figure S12. H2Aub and H3K27me3 deposition are affected by loss of MpBMI1/1L. Figure S13. Western blots of H2A and H2Aub. Figure S14. Scatter plots comparing RNA-seq triplicates. Figure S15. Scatter plots comparing ChIP-seq replicates.

Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C-4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.

The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.

Urban regeneration is an approach to revive the vitality of the communities all over the world. In China, previous regeneration efforts usually implement through a top-down method to raze the buildings and cities' historical memories. Recently, with the search for a more sustainable urban development strategy and the rise of bottom-up voices, an increasing number of stakeholders are engaged in the regeneration process. Nevertheless, the research questions of what are the roles and strategies of different stakeholders and what are the positions of the main players during the partnerships deserve in-depth examination. Embracing the strategy of culture-led waterfront regeneration, the case of Shanghai West Bund exemplifies the attempt to search for a sustainable future. Guided by the development strategy of “government-led regeneration with market-oriented management and collaborative governance”, West Bund is also an appropriate laboratory to examine the power relations among various stakeholders. Accordingly, this study includes interviews with eight key stakeholders. The current strategy indeed has merits of high-efficiency first-level development process, a favourable environment for tenants related to the culture industry, and increasing stakeholders' involvement during the collaborative governance. However, the inefficiency of secondary developers, the lacking of social impacts of cultural facilities, and the indefinite responsibilities among the administrative departments may place the small business owners and residents at a disadvantaged position. The policy recommendations provided will also target for an economically feasible, socially equitable, and culturally heritable regeneration process.

Plant genomes have large numbers of duplicated genes. After duplication one duplicate can acquire a new function or expression pattern, referred to as neofunctionalization. Some duplicated genes are imprinted, where only one allele is expressed depending on its parental origin. I hypothesized that duplicated imprinted genes frequently show an accelerated rate of amino acid sequence evolution and have a new expression pattern compared with their paralogs, which together are suggestive of neofunctionalization. I first studied four imprinted genes in Arabidopsis, FIS2, MPC, FWA, and HDG3 that have flower and/or seed specific expression. I found that they all have considerably accelerated rates of sequence evolution compared to their paralogs. To determine the ancestral expression pattern I assayed expression patterns in outgroup species, the results of which strongly suggested that the imprinted genes have acquired a novel organ-specific expression pattern restricted to flowers and/or seeds. Using data from recent large-scale identification studies of imprinted genes, I detected by phylogenetic tree analyses 133 imprinted genes that arose from gene duplication events in Brassicaceae. Analyses of 48 alpha whole genome duplicated gene pairs indicated that many imprinted genes show an accelerated rate of amino acid changes compared to their paralogs. Analyses of microarray data indicated that many imprinted genes have expression patterns restricted to flowers and/or seeds, compared with their broadly-expressed paralogs. Both the accelerated sequence rate evolution and the new expression pattern in the imprinted genes suggest that after evolutionarily recent duplication events, imprinted genes frequently underwent neofunctionalization. In particular, neofunctionalization of the FIS2 gene has led to a change in the mechanism of regulating seed development in Brassicaceae. Multiple lines of evidence, when considered together, are highly suggestive of many origins of imprinting in Brassicaceae. This study reveals that the origin of genetic imprinting can arise over short evolutionary time periods and gene duplication serves as an important factor generating imprinted genes.