Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis
Abstract Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-06142-4 |
| _version_ | 1827253952316440576 |
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| author | Li Feng Wei Yan Xianli Tang Huihui Wu Yajie Pan Dongdong Lu Qianyan Ling-hu Yuelin Liu Yongqi Liu Xiehai Song Muhammad Ali Liang Fang Hongwei Guo Bosheng Li |
| author_facet | Li Feng Wei Yan Xianli Tang Huihui Wu Yajie Pan Dongdong Lu Qianyan Ling-hu Yuelin Liu Yongqi Liu Xiehai Song Muhammad Ali Liang Fang Hongwei Guo Bosheng Li |
| author_sort | Li Feng |
| collection | DOAJ |
| description | Abstract Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants. |
| first_indexed | 2024-04-24T07:12:36Z |
| format | Article |
| id | doaj.art-0dd95e53433f4e169b91a735817aad7d |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2025-03-22T00:59:23Z |
| publishDate | 2024-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-0dd95e53433f4e169b91a735817aad7d2024-05-12T11:29:35ZengNature PortfolioCommunications Biology2399-36422024-04-017111310.1038/s42003-024-06142-4Multiple factors and features dictate the selective production of ct-siRNA in ArabidopsisLi Feng0Wei Yan1Xianli Tang2Huihui Wu3Yajie Pan4Dongdong Lu5Qianyan Ling-hu6Yuelin Liu7Yongqi Liu8Xiehai Song9Muhammad Ali10Liang Fang11Hongwei Guo12Bosheng Li13Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyInstitute of Plant and Food Science, Department of Biology, Southern University of Science and TechnologyPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in WeifangAbstract Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.https://doi.org/10.1038/s42003-024-06142-4 |
| spellingShingle | Li Feng Wei Yan Xianli Tang Huihui Wu Yajie Pan Dongdong Lu Qianyan Ling-hu Yuelin Liu Yongqi Liu Xiehai Song Muhammad Ali Liang Fang Hongwei Guo Bosheng Li Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis Communications Biology |
| title | Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis |
| title_full | Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis |
| title_fullStr | Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis |
| title_full_unstemmed | Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis |
| title_short | Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis |
| title_sort | multiple factors and features dictate the selective production of ct sirna in arabidopsis |
| url | https://doi.org/10.1038/s42003-024-06142-4 |
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