Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants. Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues in B. napus. RNA-seq: Total RNA was isolated from tissue using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. The RNA (2 ug) was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations. RNA sequencing was performed using an Illumina HiSeq X Ten platform.