BACKGROUND Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. FINDINGS We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3'-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. CONCLUSIONS We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

中文翻译：

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甘蓝型油菜H3K27me3表观基因组和转录组的全基因组分析。

背景技术已经获得了几种植物物种的组蛋白修饰的全基因组图。但是，大多数研究集中在模型系统上，并不执行FAIR数据管理原则。在这里，我们研究了甘蓝型油菜H3K27me3表观基因组和相关的转录组，这是一种在世界范围内种植的重要蔬菜。研究结果我们进行了H3K27me3染色质免疫沉淀，然后通过高强度测序和转录组学分析（通过对芜菁叶和花序的3'端RNA测序）。为了分析这些数据，我们使用Galaxy和Jupyter开发了可重现的表观基因组分析管道，并将其打包到Docker映像中，以促进透明度和重用。我们发现，H3K27me3涵盖了所有B. rapa蛋白编码基因的大约三分之一，并且它的存在与低转录水平相关。叶片和花序之间的比较分析表明，发育过程中各种花卉调控基因的表达取决于H3K27me3。为了证明H3K27me3对于B. rapa发育的重要性，我们表征了一个缺乏H3K27甲基转移酶活性的突变株。我们发现braA.clf突变植物表现出多效性的改变，例如，由于在AGAMOUS样基因座处表达的增加和H3K27me3水平的降低，卷曲的叶子。结论我们在全基因组水平上表征了表观遗传标记H3K27me3，并为其在芜菁双歧杆菌发育中的相关性提供了遗传学证据。我们的工作揭示了B. rapa中H3K27me3的表观基因组格局，并提供了新颖的基因组数据集和生物信息学分析资源。