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Journal of Integrative Agriculture  2023, Vol. 22 Issue (10): 2961-2980    DOI: 10.1016/j.jia.2023.02.024
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Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize
XIE Si-di1*, TIAN Ran1*, ZHANG Jun-jie2, LIU Han-mei2, LI Yang-ping1, HU Yu-feng1, YU Guo-wu3, HUANG Yu-bi1#, LIU Ying-hong4#
1 State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 College of Life Science, Sichuan Agricultural University, Ya’an 625014, P.R.China
3 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China
4 Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
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染色质可及性在基因转录调控中起着至关重要作用。然而,染色质可及性的调控机制,及其调控玉米关键基因表达和籽粒发育的机制尚不清楚。本研究中,我们分离了一个玉米籽粒突变体,将其命名为dek219,该突变体表现为粉质胚乳和胚停止发育。Dek219编码DICER-LIKE1 (DCL1)蛋白,一种miRNA生物发生的必需酶。Dek219功能缺失导致大多数miRNAs和组蛋白基因的表达水平显著降低。进一步研究表明,热激转录因子Hsf17-Zm00001d016571模块可能是影响组蛋白基因表达的因素之一。转座酶可及染色质测序分析(ATAC-seq)表明,与野生型(WT)相比,dek219的染色质可及性发生了改变,这可能调控了籽粒发育中关键基因的表达。通过分析WTdek219之间的差异表达基因(DEGs)和差异可染色质区域(ACRs),我们鉴定到119个受染色质可及性调控的候选基因,包括已报道的玉米籽粒发育关键基因。综上所述,这些结果表明Dek219影响染色质可及性和关键基因的表达,是玉米籽粒发育所必需的。


Chromatin accessibility plays a vital role in gene transcriptional regulation.  However, the regulatory mechanism of chromatin accessibility, as well as its role in regulating crucial gene expression and kernel development in maize (Zea mays) are poorly understood.  In this study, we isolated a maize kernel mutant designated as defective kernel219 (dek219), which displays opaque endosperm and embryo abortion.  Dek219 encodes the DICER-LIKE1 (DCL1) protein, an essential enzyme in miRNA biogenesis.  Loss of function of Dek219 results in significant reductions in the expression levels of most miRNAs and histone genes.  Further research showed that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be one of the factors affecting the expression of histone genes.  Assay results for transposase-accessible chromatin sequencing (ATAC-seq) indicated that the chromatin accessibility of dek219 is altered compared with that of wild type (WT), which may regulate the expression of crucial genes in kernel development.  By analyzing differentially expressed genes (DEGs) and differentially accessible chromatin regions (ACRs) between WT and dek219, we identified 119 candidate genes that are regulated by chromatin accessibility, including some reported to be crucial genes for kernel development.  Taken together, these results suggest that Dek219 affects chromatin accessibility and the expression of crucial genes that are required for maize kernel development

Keywords:  maize       kernel development       chromatin accessibility       histone       miRNA  
Received: 21 October 2022   Accepted: 04 January 2023

This research was funded by the National Natural Science Foundation of China (32072071) and the National Key Research and Development Program of China (2021YFF1000304).  

About author:  XIE Si-di, E-mail:; TIAN Ran, E-mail:; #Correspondence HUANG Yu-bi, Tel: +86-28-86290875, E-mail:; LIU Ying-hong, Tel: +86-28-86290916, E-mail: * These authors contributed equally to this study.

Cite this article: 

XIE Si-di, TIAN Ran, ZHANG Jun-jie, LIU Han-mei, LI Yang-ping, HU Yu-feng, YU Guo-wu, HUANG Yu-bi, LIU Ying-hong. 2023. Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize. Journal of Integrative Agriculture, 22(10): 2961-2980.

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