4.7 Article

Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus

Journal

MOLECULAR PLANT
Volume 14, Issue 4, Pages 604-619

Publisher

CELL PRESS
DOI: 10.1016/j.molp.2020.12.020

Keywords

Brassica napus; epigenome; ChIP-seq; gene expression

Funding

  1. National Natural Science Foundation of China [31930032, 31701163, 31771422, 31771402]
  2. National Key Research and Development Program of China [2016YFD0101300, 2018YFC1604000]
  3. China Postdoctoral Science Foundation [2017M612479]
  4. Fundamental Research Funds for the Central Universities [2662018py033]
  5. National Key Laboratory of Crop Genetic Improvement [ZK201906]
  6. Program for Modern Agricultural Industrial Technology System of China [CARS-12]

Ask authors/readers for more resources

The study conducted a comprehensive analysis of the epigenome in two Brassica napus lines, revealing significant differences between the An and Cn subgenomes and distinct patterns of histone modification and DNA methylation in duplicated genes. The findings provide valuable insights into epigenetic regulation in allopolyploid plants.
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization, which drives genome evolution and contributes to the increased adaptability to diverse environments. However, a comprehensive epigenome map of Brassica napus is still unavailable. In this study, we performed integrative analysis of five histone modifications, RNA polymerase II occupancy, DNA methylation, and transcriptomes in two B. napus lines (2063A and B409), and established global maps of regulatory elements, chromatin states, and their dynamics for the whole genome (including the An and Cn subgenomes) in four tissue types (young leaf, flower bud, silique, and root) of these two lines. Approximately 65.8% of the genome was annotated with different epigenomic signals. Compared with the Cn subgenome, the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks. Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes. Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns. We identified a novel bivalent chromatin state (with H3K4me1 and H3K27me3) in B. napus that is associated with tissue-specific gene expression. Furthermore, we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels. Collectively, our findings provide a valuable epigenetic resource for allopolyploid plants.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available