RiceENCODE: a comprehensive epigenomic database as rice Encyclopedia of DNA Elements

Author: LiangXie, MinghaoLiu, LunZhao, KaiCao, PengWang, WenhaoXu, Wing-KinSung, XingwangLi and GuoliangLi

Mol Plant. 2021 Oct 4. 14(10):1604-1606

Abstract: Rice (Oryza sativa L.) is one of the most important crops in the world and a common model plant for genomic research. In recent years, the application of Hi-C, ChIA-PET, and other chromosome conformation capture technologies in rice had made it more and more important to study the epigenomics and the spatial structure of rice genomes. Epigenomics and three-dimensional (3D) genomic structures are essential in research for development and breeding. However, it is still a big challenge for many groups that lack dedicated bioinformatic personnel or sufficient computational resources to utilize such epigenetic data. In this study, we combined the published three-dimensional interactive data ChIA-PET, Hi-C, transcriptome data (RNA-Seq) and the epigenomic datasets (ChIP-Seq, ATAC-Seq, MNase-Seq, FAIRE-Seq, WGBS) to construct a comprehensive epigenomic database as rice Encyclopedia of DNA Elements.

Full Article:https://doi.org/10.1016/j.molp.2021.08.018