Work Package (WP) 1 in this project mainly covered the work concerning the first research area. In this WP, we discovered that the Arabidopsis CRWN1 proteins interacted directly with chromatin at the nuclear periphery to regulate perinuclear chromatin localization (Hu et al., 2019, doi: 10.1186/s13059-019-1694-3). Following this work, we discovered that the plant nuclear lamina was more dynamic than expected, disassembling under various abiotic stress conditions (Wang et al., 2023, doi: 10.1038/s41477-023-01457-2). In addition, we performed extended work on nuclear lamin proteins in Marchantia, which took advantage of the achievement on the Marchantia genome assembly (achieved in WP2). This work led to the functional characterization of the Marchantia CRWN1 homolog (Wang et al., 2021, doi:10.3389/fpls.2021.670306).
The work concerning the second research area consisted of three WPs (WP2-WP4). WP2 aimed to identify chromatin insulation in Marchantia, providing hints to WP3 to determine candidate insulator proteins for functional studies. In this WP, by collaborating with colleagues, we improved the Marchantia male genome assembly from a scaffold to a chromosomal level, allowing comprehensive profiling of the epigenomic landscape and 3D chromatin interaction patterns (Montgomery et al., 2020, doi:10.1016/j.cub.2019.12.015). Subsequently, we participated in collaborating projects to reveal imprinting by H3K27me3 during Marchantia reproduction (Montgomery et al., 2022, doi: 10.7554/eLife.79258) and to scaffold the female sex chromosome (Iwasaki et al., 2021, doi:10.1016/j.cub.2021.10.023).
In WP3, as initially proposed for this project, Marchantia was selected as the model species to investigate the role of plant-specific TCP transcription factors in 3D genome organization. Contrary to our initial hypothesis, our study provided novel insights by rejecting the notion of TCP factors functioning as architectural proteins in this context. However, our investigation yielded an unexpected discovery: the identification of a new type of Topologically Associating Domain (TAD) in Marchantia. This finding represents a significant departure from the established understanding of TADs, as we demonstrated for the first time that transcription factor proteins can densely bind plant TADs (Karaaslan et al., 2020, doi: 10.1038/s41477-020-00766-0).
In WP4, we characterized Marchantia transcription factors that might intensively interact with TADs as TCP. In total, eleven transcription factors’ protein-chromatin interactions have been profiled, which collectively suggests that Marchantia TADs function as hubs integrating multiple transcription factors. Besides, in a collaborating project, we discovered that Arabidopsis pds5a mutants developed prominent TAD structures across the Arabidopsis genome. We consider our finding that the Arabidopsis PDS5A protein suppresses TAD formation ground-breaking because it brings an end to the long-standing speculation about the absence of TAD structure in Arabidopsis; meanwhile, it marks the commencement of the efforts in the plant community to decipher the molecular mechanisms behind plant TAD regulation (Göbel et al., under review).
