Genome-wide analysis of the H3K27me3 epigenome and transcriptome in brassica rapa

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

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in brassica rapa

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

Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state

Reprogramming of epigenetic states in gametes and embryos is essential for correct development in plants and mammals(1). In plants, the germ line arises from somatic tissues of the flower necessitating erasure of chromatin modifications accumulated at specific loci during development or in response to external stimuli. If this occurs inefficiently it can lead to epigenetic states being inherited from one generation to the next(2-4). However, in most cases accumulated epigenetic modifications are efficiently erased before the next generation. An important example of epigenetic reprogramming in plants is the resetting of expression of the Arabidopsis thaliana floral repressor FLC locus. FLC is epigenetically silenced by prolonged cold in a process called vernalization. However, the locus is reactivated prior to completion of seed development to ensure a vernalization requirement every generation. In contrast to our detailed understanding of the Polycomb-mediated epigenetic silencing induced by vernalization, little is known about the mechanism involved in the re-activation of FLC. Here we show that a hypomorphic mutation in the jumonji domain protein ELF6 impaired the reactivation of FLC in reproductive tissues, leading to inheritance of a partially vernalized state. ELF6 has H3K27me3 demethylase activity and the mutation reduced this enzymatic activity in planta. Consistent with this, H3K27me3 levels at the FLC locus stayed higher and FLC expression remained lower, than in the wild type in the following generation. Our data reveal an ancient role for H3K27 demethylation in the reprogramming of epigenetic states in plant and mammalian embryos(5-7)