MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae
The Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulate...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1256186/full |
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| author | Dipro Sinha Dipro Sinha Tanwy Dasmandal Tanwy Dasmandal Tanwy Dasmandal Krishnayan Paul Krishnayan Paul Md Yeasin Sougata Bhattacharjee Sougata Bhattacharjee Sougata Bhattacharjee Sneha Murmu Dwijesh Chandra Mishra Soumen Pal Anil Rai Sunil Archak |
| author_facet | Dipro Sinha Dipro Sinha Tanwy Dasmandal Tanwy Dasmandal Tanwy Dasmandal Krishnayan Paul Krishnayan Paul Md Yeasin Sougata Bhattacharjee Sougata Bhattacharjee Sougata Bhattacharjee Sneha Murmu Dwijesh Chandra Mishra Soumen Pal Anil Rai Sunil Archak |
| author_sort | Dipro Sinha |
| collection | DOAJ |
| description | The Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulates gene expression, through predicting methylation sites of their promoters particularly in major crop species. In this study, we developed a user-friendly prediction server for accurate prediction of 6mA sites by incorporating a robust feature set, viz., Binary Encoding of Mono-nucleotide DNA. Our model,MethSemble-6mA, outperformed other state-of-the-art tools in terms of accuracy (93.12%). Furthermore, we investigated the pattern of probable 6mA sites at the upstream promoter regions of the LBD-containing genes in Triticum aestivum and its allied species using the developed tool. On average, each selected species had four 6mA sites, and it was found that with speciation and due course of evolution in wheat, the frequency of methylation have reduced, and a few sites remain conserved. This obviously cues gene birth and gene expression alteration through methylation over time in a species and reflects functional conservation throughout evolution. Since DNA methylation is a vital event in almost all plant developmental processes (e.g., genomic imprinting and gametogenesis) along with other life processes, our findings on epigenetic regulation of LBD-containing genes have dynamic implications in basic and applied research. Additionally, MethSemble-6mA (http://cabgrid.res.in:5799/) will serve as a useful resource for a plant breeders who are interested to pursue epigenetic-based crop improvement research. |
| first_indexed | 2024-03-11T19:11:56Z |
| format | Article |
| id | doaj.art-42b8d8f6198e4a4883f4d03e1f2110fc |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-11T19:11:56Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-42b8d8f6198e4a4883f4d03e1f2110fc2023-10-09T11:08:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-10-011410.3389/fpls.2023.12561861256186MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in PoaceaeDipro Sinha0Dipro Sinha1Tanwy Dasmandal2Tanwy Dasmandal3Tanwy Dasmandal4Krishnayan Paul5Krishnayan Paul6Md Yeasin7Sougata Bhattacharjee8Sougata Bhattacharjee9Sougata Bhattacharjee10Sneha Murmu11Dwijesh Chandra Mishra12Soumen Pal13Anil Rai14Sunil Archak15ICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaGraduate School, ICAR-Indian Agricultural Research Institute, Delhi, IndiaICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaGraduate School, ICAR-Indian Agricultural Research Institute, Delhi, IndiaICAR-National Bureau of Fish Genetic Resources, Lucknow, IndiaGraduate School, ICAR-Indian Agricultural Research Institute, Delhi, IndiaICAR-National Institute for Plant Biotechnology, Delhi, IndiaICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaGraduate School, ICAR-Indian Agricultural Research Institute, Delhi, IndiaICAR-National Institute for Plant Biotechnology, Delhi, IndiaICAR-Indian Agricultural Research Institute, Hazaribagh, Jharkhand, IndiaICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaICAR-Indian Agricultural Statistics Research Institute, Delhi, IndiaIndian Council of Agricultural Research, Delhi, IndiaICAR-National Bureau of Plant Genetic Resources, Delhi, IndiaThe Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulates gene expression, through predicting methylation sites of their promoters particularly in major crop species. In this study, we developed a user-friendly prediction server for accurate prediction of 6mA sites by incorporating a robust feature set, viz., Binary Encoding of Mono-nucleotide DNA. Our model,MethSemble-6mA, outperformed other state-of-the-art tools in terms of accuracy (93.12%). Furthermore, we investigated the pattern of probable 6mA sites at the upstream promoter regions of the LBD-containing genes in Triticum aestivum and its allied species using the developed tool. On average, each selected species had four 6mA sites, and it was found that with speciation and due course of evolution in wheat, the frequency of methylation have reduced, and a few sites remain conserved. This obviously cues gene birth and gene expression alteration through methylation over time in a species and reflects functional conservation throughout evolution. Since DNA methylation is a vital event in almost all plant developmental processes (e.g., genomic imprinting and gametogenesis) along with other life processes, our findings on epigenetic regulation of LBD-containing genes have dynamic implications in basic and applied research. Additionally, MethSemble-6mA (http://cabgrid.res.in:5799/) will serve as a useful resource for a plant breeders who are interested to pursue epigenetic-based crop improvement research.https://www.frontiersin.org/articles/10.3389/fpls.2023.1256186/full6mAensemble modelDNA methylationMethSemble-6mALBD genewheat |
| spellingShingle | Dipro Sinha Dipro Sinha Tanwy Dasmandal Tanwy Dasmandal Tanwy Dasmandal Krishnayan Paul Krishnayan Paul Md Yeasin Sougata Bhattacharjee Sougata Bhattacharjee Sougata Bhattacharjee Sneha Murmu Dwijesh Chandra Mishra Soumen Pal Anil Rai Sunil Archak MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae Frontiers in Plant Science 6mA ensemble model DNA methylation MethSemble-6mA LBD gene wheat |
| title | MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae |
| title_full | MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae |
| title_fullStr | MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae |
| title_full_unstemmed | MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae |
| title_short | MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae |
| title_sort | methsemble 6ma an ensemble based 6ma prediction server and its application on promoter region of lbd gene family in poaceae |
| topic | 6mA ensemble model DNA methylation MethSemble-6mA LBD gene wheat |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1256186/full |
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