Advances deciphering the epigenome of plants

Epigenetic regulation in plants has enormous implications for crop improvement and agriculture. Researchers at Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) used next-generation sequencing approaches and novel computational analytical pipelines to describe the genome-wide map of an epigenetic mark in a Brassica crop.


The term epigenome refers to the set of regulatory modifications that alters DNA or histones in the nucleus. These epigenetic modifications have regulatory functions on the expression of genes and the organization of the genome. In other words, we can think of the DNA sequence as the “hardware” and epigenomic information as the “software” that controls the genome.

The specific histone methylation H3K27me3 is an epigenetic mark crucial for animal and plant development. However, epigenomic studies focused on crop plant species are extremely scarce. To understand the epigenetic regulation underlying key agronomic traits in Brassica crops, researchers at CBGP have obtained the genome-wide map of H3K27me3 from an oilseed Brassica rapa variety, an important vegetable cultivated world-wide.

This study was recently published in the journal GigaScience, resulting from a fruitful collaboration between the BIOLOGICAL INFORMATICS and EPIGENETIC REGULATION OF AGRONOMIC TRAITS laboratories under the CBGP-Severo Ochoa transversal scientific program. In this work, the authors performed epigenomic and transcriptomic high-throughput sequencing (ChIP-seq and RNA-seq) from different B. rapa tissue samples. To analyze these complex genomic data, they developed the “Reproducible Epigenomic Analysis” bioinformatic pipeline, which has been made publicly available to facilitate transparency and reproducibility in conformance with the FAIR data principles (findability, accessibility, interoperability and reusability).

To sum up, this work reveals the epigenomic landscape of H3K27me3 in B. rapa providing novel genomic bioinformatics tools, and it will lead the way to further epigenomic studies in the complex genome of other Brassica crops like cauliflower or oilseed rape.


Original Paper:

Payá-Milans, M., Poza-Viejo, L., Martín-Uriz, P.S., Lara-Astiaso, D., Wilkinson, M.D., Crevillén, P. 2019. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. GigaScience 8. DOI: 10.1093/gigascience/giz147