Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-10-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311923000369 |
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| author | Si-di XIE Ran TIAN Jun-jie ZHANG Han-mei LIU Yang-ping LI Yu-feng HU Guo-wu YU Yu-bi HUANG Ying-hong LIU |
| author_facet | Si-di XIE Ran TIAN Jun-jie ZHANG Han-mei LIU Yang-ping LI Yu-feng HU Guo-wu YU Yu-bi HUANG Ying-hong LIU |
| author_sort | Si-di XIE |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T18:28:41Z |
| format | Article |
| id | doaj.art-3254d2b7f52d45aab314f9532ea7b8e4 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-03-11T18:28:41Z |
| publishDate | 2023-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-3254d2b7f52d45aab314f9532ea7b8e42023-10-13T13:53:12ZengElsevierJournal of Integrative Agriculture2095-31192023-10-01221029612980Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maizeSi-di XIE0Ran TIAN1Jun-jie ZHANG2Han-mei LIU3Yang-ping LI4Yu-feng HU5Guo-wu YU6Yu-bi HUANG7Ying-hong LIU8State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.ChinaCollege of Life Science, Sichuan Agricultural University, Ya'an 625014, P.R.ChinaCollege of Life Science, Sichuan Agricultural University, Ya'an 625014, P.R.ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.ChinaCollege of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Correspondence HUANG Yu-bi, Tel: +86-28-86290875Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China; Correspondence LIU Ying-hong, Tel: +86-28-86290916Chromatin 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.http://www.sciencedirect.com/science/article/pii/S2095311923000369maizekernel developmentchromatin accessibilityhistonemiRNA |
| spellingShingle | Si-di XIE Ran TIAN Jun-jie ZHANG Han-mei LIU Yang-ping LI Yu-feng HU Guo-wu YU Yu-bi HUANG Ying-hong LIU Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize Journal of Integrative Agriculture maize kernel development chromatin accessibility histone miRNA |
| title | Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize |
| title_full | Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize |
| title_fullStr | Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize |
| title_full_unstemmed | Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize |
| title_short | Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize |
| title_sort | dek219 encodes the dicer like1 protein that affects chromatin accessibility and kernel development in maize |
| topic | maize kernel development chromatin accessibility histone miRNA |
| url | http://www.sciencedirect.com/science/article/pii/S2095311923000369 |
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