Intragenic heterochromatin‐mediated alternative polyadenylation modulates miRNA and pollen development in rice

Abstract

Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear.Intragenic heterochromatin can be recognized by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation.• Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development.• We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of miRNA precursor, to promote the processing of full-length OsXRNL and regulates miRNA abundance. Accepted ArticleThis article is protected by copyright. All rights reservedWe found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterized rice AAE complex and its involvement in alternative polyadenylation and pollen development.• Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

“…In recent years, studies on plant ncRNAs have mainly focused on lncRNAs, circRNAs and miRNAs ( Dou et al, 2017 ; Wang et al, 2018 , 2021c ; Li et al, 2020 ; You et al, 2021 ; Zhou et al, 2021 ). Due to the differences in the sources and functions of these three types of ncRNAs, they play a role in various plant growth and development processes ( Voinnet, 2009 ; Tang and Chu, 2017 ; Zhai et al, 2020 ; Chand Jha et al, 2021 ).…”

“…In the past few years, several research groups have reported that some miRNAs are involved in regulating rice growth, development and the morphogenesis of shoot architecture ( Tang and Chu, 2017 ; Qiao et al, 2021 ). OsASI1 is involved in the processing of a miRNA precursor and regulates the abundance of miRNA, which is essential for rice pollen development and flowering ( You et al, 2021 ). Rice miRNAs can coordinate both immune and agronomic traits.…”

Epigenetic Dynamics and Regulation of Plant Male Reproduction

“…The protein complex ASI1 (Antisilencing 1)–AIPP1 (ASI1-Immunoprecipitated Protein 1)–EDM2 (Enhanced Downy Mildew 2) recognizes intragenic heterochromatin and regulates alternative polyadenylation in Arabidopsis [ 92 ]. The loss of rice OsASI1 impacts the poly(A) site usage of a large number of genes, particularly heterochromatic element-marked genes, leading to severe developmental defects in pollen [ 82 ]. OsPEM1 (Pollen Expressed MBD like 1), a methyl-CpG-binding domain (MBD) family protein, members of which have been identified as important DNA methylation “readers” in animals, is a new master regulator of pollen exine development.…”

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice

“…Taken together, these reports indicate that proteins containing BAH domains and RRMs play pivotal roles in developmental processes. A recent study showed that OsASI1 (the orthologue of Arabidopsis ASI1 in rice) regulates a nuclear XRN family exonuclease gene, OsXRNL , which further affects the processing of miRNA precursors (You et al ., 2021 ). However, the functions of proteins containing BAH domains and RRMs in the regulation of tiller number remain unknown.…”