Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling
In animals and plants, circRNAs regulate gene expression and act as sponges that inhibit the activity of microRNAs. This study aimed to determine how specific circRNAs are expressed in rice grains at different stages of grain filling, under normal and low light conditions. We extracted total RNA fro...
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MDPI AG
2022-05-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/9/1272 |
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| author | Hong Chen Tao Wang Zhiyou Gong Hui Lu Yong Chen Fei Deng Wanjun Ren |
| author_facet | Hong Chen Tao Wang Zhiyou Gong Hui Lu Yong Chen Fei Deng Wanjun Ren |
| author_sort | Hong Chen |
| collection | DOAJ |
| description | In animals and plants, circRNAs regulate gene expression and act as sponges that inhibit the activity of microRNAs. This study aimed to determine how specific circRNAs are expressed in rice grains at different stages of grain filling, under normal and low light conditions. We extracted total RNA from rice grains under low and sufficient light conditions. Deep sequencing was performed using circRNA libraries, and bioinformatics tools were used to identify the circRNAs. In addition, we analyzed targeted messenger RNA functions using two databases to predict the processes involved in rice grain development, and we conducted real-time PCR on 15 of the circRNAs as well as Sanger sequencing. During the grain development process, 8015 candidate circRNAs were isolated, among which the number of known circRNAs was 1661. We also found that the number of circRNAs changed with the time of development. Among them, six circRNAs acted as sponges that targeted more than two microRNAs at different stages of development, and these circRNAs showed a regulatory pattern consistent with the transcriptome sequencing results. More circRNA diversity was found under low light treatment compared to normal light. These findings reveal a possible link between circRNA regulation and the expression of the functional genes associated with photosignal-mediated rice grain development. |
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| language | English |
| last_indexed | 2024-03-10T03:47:55Z |
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| spelling | doaj.art-77c9e37422d645ab9bbdf5cc680129582023-11-23T09:03:58ZengMDPI AGPlants2223-77472022-05-01119127210.3390/plants11091272Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain FillingHong Chen0Tao Wang1Zhiyou Gong2Hui Lu3Yong Chen4Fei Deng5Wanjun Ren6Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaKey Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, ChinaIn animals and plants, circRNAs regulate gene expression and act as sponges that inhibit the activity of microRNAs. This study aimed to determine how specific circRNAs are expressed in rice grains at different stages of grain filling, under normal and low light conditions. We extracted total RNA from rice grains under low and sufficient light conditions. Deep sequencing was performed using circRNA libraries, and bioinformatics tools were used to identify the circRNAs. In addition, we analyzed targeted messenger RNA functions using two databases to predict the processes involved in rice grain development, and we conducted real-time PCR on 15 of the circRNAs as well as Sanger sequencing. During the grain development process, 8015 candidate circRNAs were isolated, among which the number of known circRNAs was 1661. We also found that the number of circRNAs changed with the time of development. Among them, six circRNAs acted as sponges that targeted more than two microRNAs at different stages of development, and these circRNAs showed a regulatory pattern consistent with the transcriptome sequencing results. More circRNA diversity was found under low light treatment compared to normal light. These findings reveal a possible link between circRNA regulation and the expression of the functional genes associated with photosignal-mediated rice grain development.https://www.mdpi.com/2223-7747/11/9/1272ricecircular RNAlight |
| spellingShingle | Hong Chen Tao Wang Zhiyou Gong Hui Lu Yong Chen Fei Deng Wanjun Ren Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling Plants rice circular RNA light |
| title | Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling |
| title_full | Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling |
| title_fullStr | Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling |
| title_full_unstemmed | Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling |
| title_short | Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling |
| title_sort | low light conditions alter genome wide profiles of circular rnas in rice grains during grain filling |
| topic | rice circular RNA light |
| url | https://www.mdpi.com/2223-7747/11/9/1272 |
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