J Integr Plant Biol. ›› 2021, Vol. 63 ›› Issue (4): 707-722.DOI: 10.1111/jipb.13068

Special Issue: Epigenetics

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Genome‐wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

Yi‐Zhe Zhang1,2†, Juncheng Lin3†, Zhizhong Ren1†, Chun‐Xiang Chen1,2†, Daisuke Miki1†, Si‐Si Xie1,2, Jian Zhang1,2, Ya‐Nan Chang1,2, Jing Jiang4, Jun Yan5, Qingshun Q. Li3,6*, Jian‐Kang Zhu1,7* and Cheng‐Guo Duan1,4*   

  1. 1Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
    2University of Chinese Academy of Sciences, Beijing 100049, China
    3Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
    4State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
    5School of Life Sciences, East China Normal University, Shanghai 200241, China
    6Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona 91766, USA
    7Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette 47907, USA

    These authors contributed equally to this work.
    *Correspondences: Qingshun Q. Li (liqq@xmu.edu.cn); Jian‐Kang Zhu (jkzhu@psc.ac.cn); Cheng‐Guo Duan (cgduan@psc.ac.cn, Dr. Duan is fully responsible for the distribution of all materials associated with this article)
  • Received:2020-10-30 Accepted:2020-12-30 Online:2021-01-12 Published:2021-04-01

Abstract: Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1‐AIPP1‐EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin‐containing genes. However, the genome‐wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome‐wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin‐containing genes, including not only intronic heterochromatin‐containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin‐overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin‐containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.

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