Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan.
Curr Biol. 2020 Feb 24;30(4):573-588.e7. doi: 10.1016/j.cub.2019.12.015. Epub 2020 Jan 30.
Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, and read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives of ancestors of the main groups of eukaryotes, and our knowledge of the evolution of chromatin-related processes is limited. We used the bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and three-dimensional genome organization in an early diverging land plant lineage. Based on genomic profiles of ten chromatin marks, we conclude that the relationship between active marks and gene expression is conserved across land plants. In contrast, we observed distinctive features of transposons and other repetitive sequences in Marchantia compared with flowering plants. Silenced transposons and repeats did not accumulate around centromeres. Although a large fraction of constitutive heterochromatin was marked by H3K9 methylation as in flowering plants, a significant proportion of transposons were marked by H3K27me3, which is otherwise dedicated to the transcriptional repression of protein-coding genes in flowering plants. Chromatin compartmentalization analyses of Hi-C data revealed that repressed B compartments were densely decorated with H3K27me3 but not H3K9 or DNA methylation as reported in flowering plants. We conclude that, in early plants, H3K27me3 played an essential role in heterochromatin function, suggesting an ancestral role of this mark in transposon silencing.
核小体介导的基因组包装是真核生物的一个标志。组蛋白及其沉积、去除和读取组蛋白修饰的途径是高度保守的。然而，我们缺乏关于现存真核生物主要类群祖先代表的染色质景观的信息，我们对与染色质相关过程的进化的了解也有限。我们使用了苔藓植物 Marchantia polymorpha，它与维管植物大约在 4 亿年前分化，以获得一个全染色体基因组组装，并探索早期分化的陆地植物谱系中的染色质景观和三维基因组组织。基于十个染色质标记的基因组特征，我们得出结论，活性标记与基因表达之间的关系在陆地植物中是保守的。相比之下，与开花植物相比，我们观察到 Marchantia 中转座子和其他重复序列的独特特征。沉默的转座子和重复序列不会在着丝粒周围积累。尽管大量组成型异染色质如在开花植物中那样被 H3K9 甲基化标记，但相当一部分转座子被 H3K27me3 标记，而 H3K27me3 通常专门用于开花植物中蛋白质编码基因的转录抑制。Hi-C 数据的染色质区室分析表明，受抑制的 B 区室被 H3K27me3 密集修饰，但不像在开花植物中那样被 H3K9 或 DNA 甲基化修饰。我们得出的结论是，在早期植物中，H3K27me3 在异染色质功能中发挥了重要作用，这表明该标记在转座子沉默中的一个古老作用。
