Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa.
The current "small interfering RNA(siRNA)→Target" mining tools can only search for targets of known siRNAs, and cannot discover co-regulatory siRNAs of unknown sequences that may exist, which means that the "microRNA(miRNA)→Target" database obtained by these mining tools is incom...
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| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0321182 |
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| author | Zhihong Yang Lan Yu Yeqing Jiang Yijun Meng Chaogang Shao |
| author_facet | Zhihong Yang Lan Yu Yeqing Jiang Yijun Meng Chaogang Shao |
| author_sort | Zhihong Yang |
| collection | DOAJ |
| description | The current "small interfering RNA(siRNA)→Target" mining tools can only search for targets of known siRNAs, and cannot discover co-regulatory siRNAs of unknown sequences that may exist, which means that the "microRNA(miRNA)→Target" database obtained by these mining tools is incomplete. Using the previously developed sRNATargetDigger, we re-mined the rice "miRNA→Target" database supported by the degradome and found 86.2% of the target genes were co-regulated by one or more miRNAs\siRNAs. Besides the known miRNAs, 30 miRNA isoforms (isomiRs) and 12 siRNAs were identified to be involved in co-regulation, which play important roles in rice response to external auxin regulation, rice blast resistance, adventitious root formation, cold resistance, and tillering etc. Some isomiRs even have higher expression levels than miRNAs. In addition, we also found that the regulatory relationship between 51 miRNAs and 48 target genes in the original database could not be verified due to the low expression levels of miRNA, poor complementarity between miRNA and target, or no specific cleavage signal detected by degradome in the middle of the miRNA binding site in the targets. Four miRNAs (osa-miR530-5p,osa-miR319b,osa-miR172c and osa-miR395a) only found isomiRs involved in regulation. In addition, we also found a number of miRNA→target regulatory relationships missed in the database. This study improved the rice "miRNA→target" database which will contribute to the research of rice miRNA and molecular breeding. |
| format | Article |
| id | doaj-art-abdff7c1140f4fcca30447e25d402683 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj-art-abdff7c1140f4fcca30447e25d4026832025-08-20T02:16:15ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01204e032118210.1371/journal.pone.0321182Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa.Zhihong YangLan YuYeqing JiangYijun MengChaogang ShaoThe current "small interfering RNA(siRNA)→Target" mining tools can only search for targets of known siRNAs, and cannot discover co-regulatory siRNAs of unknown sequences that may exist, which means that the "microRNA(miRNA)→Target" database obtained by these mining tools is incomplete. Using the previously developed sRNATargetDigger, we re-mined the rice "miRNA→Target" database supported by the degradome and found 86.2% of the target genes were co-regulated by one or more miRNAs\siRNAs. Besides the known miRNAs, 30 miRNA isoforms (isomiRs) and 12 siRNAs were identified to be involved in co-regulation, which play important roles in rice response to external auxin regulation, rice blast resistance, adventitious root formation, cold resistance, and tillering etc. Some isomiRs even have higher expression levels than miRNAs. In addition, we also found that the regulatory relationship between 51 miRNAs and 48 target genes in the original database could not be verified due to the low expression levels of miRNA, poor complementarity between miRNA and target, or no specific cleavage signal detected by degradome in the middle of the miRNA binding site in the targets. Four miRNAs (osa-miR530-5p,osa-miR319b,osa-miR172c and osa-miR395a) only found isomiRs involved in regulation. In addition, we also found a number of miRNA→target regulatory relationships missed in the database. This study improved the rice "miRNA→target" database which will contribute to the research of rice miRNA and molecular breeding.https://doi.org/10.1371/journal.pone.0321182 |
| spellingShingle | Zhihong Yang Lan Yu Yeqing Jiang Yijun Meng Chaogang Shao Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. PLoS ONE |
| title | Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. |
| title_full | Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. |
| title_fullStr | Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. |
| title_full_unstemmed | Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. |
| title_short | Identification of the co-regulatory siRNAs of "miRNA→target" in Oryza sativa. |
| title_sort | identification of the co regulatory sirnas of mirna target in oryza sativa |
| url | https://doi.org/10.1371/journal.pone.0321182 |
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