Long non-coding RNAs as the regulatory hubs in rice response to salt stress
Abstract Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (sa...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-26133-x |
| _version_ | 1797980332291522560 |
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| author | Raheleh Mirdar Mansuri Amir-Hossein Azizi Amir-Hossein Sadri Zahra-Sadat Shobbar |
| author_facet | Raheleh Mirdar Mansuri Amir-Hossein Azizi Amir-Hossein Sadri Zahra-Sadat Shobbar |
| author_sort | Raheleh Mirdar Mansuri |
| collection | DOAJ |
| description | Abstract Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq in root tissues at seedling stage. In FL478 and IR29, 8724 and 9235 transcripts with length of > 200 bp were nominated as potential lncRNAs, respectively. Rigorous filtering left four (in FL478) and nine (in IR29) DE-lncRNAs with only 2 DE-lncRNAs in common. ATAC-seq data showed that the genomic regions of all four lncRNAs in FL478 and 6/9 in IR29 are significantly accessible for transcription. Weighted correlation network analysis (WGCNA) revealed that lncRNA.2-FL was highly correlated with 173 mRNAs as trans-targets and a gene encoding pentatricopeptide repeat (PPR) protein was predicted as cis-target of lncRNA.2-FL. In silico mutagenesis analysis proposed the same transcription factor binding sites (TFBSs) in vicinity of the trans- and cis-regulatory target genes of lncRNA.2-FL, which significantly affect their transcription start site (TSS). This study provides new insights into involvement of the DE-lncRNAs in rice response to salt stress. Among them, lncRNA.2-FL may play a significant regulatory role in the salt stress tolerance of FL478. |
| first_indexed | 2024-04-11T05:52:50Z |
| format | Article |
| id | doaj.art-10dbcb8a6bdb4b1a860df1b58d9dd460 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T05:52:50Z |
| publishDate | 2022-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-10dbcb8a6bdb4b1a860df1b58d9dd4602022-12-22T04:42:00ZengNature PortfolioScientific Reports2045-23222022-12-0112111410.1038/s41598-022-26133-xLong non-coding RNAs as the regulatory hubs in rice response to salt stressRaheleh Mirdar Mansuri0Amir-Hossein Azizi1Amir-Hossein Sadri2Zahra-Sadat Shobbar3Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII)Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII)Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII)Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII)Abstract Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq in root tissues at seedling stage. In FL478 and IR29, 8724 and 9235 transcripts with length of > 200 bp were nominated as potential lncRNAs, respectively. Rigorous filtering left four (in FL478) and nine (in IR29) DE-lncRNAs with only 2 DE-lncRNAs in common. ATAC-seq data showed that the genomic regions of all four lncRNAs in FL478 and 6/9 in IR29 are significantly accessible for transcription. Weighted correlation network analysis (WGCNA) revealed that lncRNA.2-FL was highly correlated with 173 mRNAs as trans-targets and a gene encoding pentatricopeptide repeat (PPR) protein was predicted as cis-target of lncRNA.2-FL. In silico mutagenesis analysis proposed the same transcription factor binding sites (TFBSs) in vicinity of the trans- and cis-regulatory target genes of lncRNA.2-FL, which significantly affect their transcription start site (TSS). This study provides new insights into involvement of the DE-lncRNAs in rice response to salt stress. Among them, lncRNA.2-FL may play a significant regulatory role in the salt stress tolerance of FL478.https://doi.org/10.1038/s41598-022-26133-x |
| spellingShingle | Raheleh Mirdar Mansuri Amir-Hossein Azizi Amir-Hossein Sadri Zahra-Sadat Shobbar Long non-coding RNAs as the regulatory hubs in rice response to salt stress Scientific Reports |
| title | Long non-coding RNAs as the regulatory hubs in rice response to salt stress |
| title_full | Long non-coding RNAs as the regulatory hubs in rice response to salt stress |
| title_fullStr | Long non-coding RNAs as the regulatory hubs in rice response to salt stress |
| title_full_unstemmed | Long non-coding RNAs as the regulatory hubs in rice response to salt stress |
| title_short | Long non-coding RNAs as the regulatory hubs in rice response to salt stress |
| title_sort | long non coding rnas as the regulatory hubs in rice response to salt stress |
| url | https://doi.org/10.1038/s41598-022-26133-x |
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