A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance
Abstract Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-02-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-28836-1 |
| _version_ | 1811165964124815360 |
|---|---|
| author | Deepa Jaganathan Raja Rajakani Dadakhalandar Doddamani Divya Saravanan Shalini Pulipati Vivek Hari Sundar G Gothandapani Sellamuthu Shilpha Jayabalan Kumkum Kumari Pavithra Parthasarathy Punitha S. Sivaprakash Ramalingam Padubidri V. Shivaprasad Gayatri Venkataraman |
| author_facet | Deepa Jaganathan Raja Rajakani Dadakhalandar Doddamani Divya Saravanan Shalini Pulipati Vivek Hari Sundar G Gothandapani Sellamuthu Shilpha Jayabalan Kumkum Kumari Pavithra Parthasarathy Punitha S. Sivaprakash Ramalingam Padubidri V. Shivaprasad Gayatri Venkataraman |
| author_sort | Deepa Jaganathan |
| collection | DOAJ |
| description | Abstract Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the ‘A10234287911’ allele may promote better processing vis-à-vis the structure conferred by ‘G10234287911’ allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression. |
| first_indexed | 2024-04-10T15:44:42Z |
| format | Article |
| id | doaj.art-dd11cd8706044db386d0049b95af663a |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T15:44:42Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-dd11cd8706044db386d0049b95af663a2023-02-12T12:11:48ZengNature PortfolioScientific Reports2045-23222023-02-0113111610.1038/s41598-023-28836-1A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundanceDeepa Jaganathan0Raja Rajakani1Dadakhalandar Doddamani2Divya Saravanan3Shalini Pulipati4Vivek Hari Sundar G5Gothandapani Sellamuthu6Shilpha Jayabalan7Kumkum Kumari8Pavithra Parthasarathy9Punitha S.10Sivaprakash Ramalingam11Padubidri V. Shivaprasad12Gayatri Venkataraman13Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)The Roslin Institute, University of EdinburghTamil Nadu Agricultural University (TNAU)Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)National Centre for Biological Sciences, Tata Institute of Fundamental ResearchPlant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)GIS and Remote Sensing Laboratory, M. S. Swaminathan Research Foundation (MSSRF)CSIR-IGIBNational Centre for Biological Sciences, Tata Institute of Fundamental ResearchPlant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF)Abstract Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the ‘A10234287911’ allele may promote better processing vis-à-vis the structure conferred by ‘G10234287911’ allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.https://doi.org/10.1038/s41598-023-28836-1 |
| spellingShingle | Deepa Jaganathan Raja Rajakani Dadakhalandar Doddamani Divya Saravanan Shalini Pulipati Vivek Hari Sundar G Gothandapani Sellamuthu Shilpha Jayabalan Kumkum Kumari Pavithra Parthasarathy Punitha S. Sivaprakash Ramalingam Padubidri V. Shivaprasad Gayatri Venkataraman A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance Scientific Reports |
| title | A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance |
| title_full | A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance |
| title_fullStr | A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance |
| title_full_unstemmed | A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance |
| title_short | A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance |
| title_sort | conserved snp variation in the pre mir396c flanking region in oryza sativa indica landraces correlates with mature mirna abundance |
| url | https://doi.org/10.1038/s41598-023-28836-1 |
| work_keys_str_mv | AT deepajaganathan aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT rajarajakani aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT dadakhalandardoddamani aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT divyasaravanan aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT shalinipulipati aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT vivekharisundarg aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT gothandapanisellamuthu aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT shilphajayabalan aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT kumkumkumari aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT pavithraparthasarathy aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT punithas aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT sivaprakashramalingam aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT padubidrivshivaprasad aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT gayatrivenkataraman aconservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT deepajaganathan conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT rajarajakani conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT dadakhalandardoddamani conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT divyasaravanan conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT shalinipulipati conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT vivekharisundarg conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT gothandapanisellamuthu conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT shilphajayabalan conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT kumkumkumari conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT pavithraparthasarathy conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT punithas conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT sivaprakashramalingam conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT padubidrivshivaprasad conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance AT gayatrivenkataraman conservedsnpvariationinthepremir396cflankingregioninoryzasativaindicalandracescorrelateswithmaturemirnaabundance |