Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles
<p>Abstract</p> <p>Background</p> <p>Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although <it>Solanum lycopersicum&l...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2013-01-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/14/57 |
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| author | Aiese Cigliano Riccardo Sanseverino Walter Cremona Gaetana Ercolano Maria R Conicella Clara Consiglio Federica M |
| author_facet | Aiese Cigliano Riccardo Sanseverino Walter Cremona Gaetana Ercolano Maria R Conicella Clara Consiglio Federica M |
| author_sort | Aiese Cigliano Riccardo |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although <it>Solanum lycopersicum</it> is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (<it>HMs</it>) in tomato are sketchy.</p> <p>Results</p> <p>Based on recently released tomato whole-genome sequences, we identified <it>in silico</it> 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (<it>Arabidopsis thaliana</it>), maize (<it>Zea mays</it>) and rice (<it>Oryza sativa</it>) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of <it>HMs</it> within tomato organs revealed a broad functional role for some <it>HMs</it> and a more specific activity for others, suggesting key <it>HM</it> regulators in tomato development. Finally, we explored <it>S. pennellii</it> introgression lines (ILs) and integrated the map position of <it>HMs</it>, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify <it>HM</it> candidates involved in carotenoid biosynthesis in tomato fruits.</p> <p>Conclusions</p> <p>In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of <it>HMs</it> in other <it>Solanaceae</it> species.</p> |
| first_indexed | 2024-12-11T00:21:57Z |
| format | Article |
| id | doaj.art-cb57ffc514fd46ac98c88396f240edd8 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T00:21:57Z |
| publishDate | 2013-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-cb57ffc514fd46ac98c88396f240edd82022-12-22T01:27:43ZengBMCBMC Genomics1471-21642013-01-011415710.1186/1471-2164-14-57Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental rolesAiese Cigliano RiccardoSanseverino WalterCremona GaetanaErcolano Maria RConicella ClaraConsiglio Federica M<p>Abstract</p> <p>Background</p> <p>Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although <it>Solanum lycopersicum</it> is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (<it>HMs</it>) in tomato are sketchy.</p> <p>Results</p> <p>Based on recently released tomato whole-genome sequences, we identified <it>in silico</it> 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (<it>Arabidopsis thaliana</it>), maize (<it>Zea mays</it>) and rice (<it>Oryza sativa</it>) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of <it>HMs</it> within tomato organs revealed a broad functional role for some <it>HMs</it> and a more specific activity for others, suggesting key <it>HM</it> regulators in tomato development. Finally, we explored <it>S. pennellii</it> introgression lines (ILs) and integrated the map position of <it>HMs</it>, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify <it>HM</it> candidates involved in carotenoid biosynthesis in tomato fruits.</p> <p>Conclusions</p> <p>In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of <it>HMs</it> in other <it>Solanaceae</it> species.</p>http://www.biomedcentral.com/1471-2164/14/57<it>Solanum lycopersicum</it>EpigeneticsDevelopment |
| spellingShingle | Aiese Cigliano Riccardo Sanseverino Walter Cremona Gaetana Ercolano Maria R Conicella Clara Consiglio Federica M Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles BMC Genomics <it>Solanum lycopersicum</it> Epigenetics Development |
| title | Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles |
| title_full | Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles |
| title_fullStr | Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles |
| title_full_unstemmed | Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles |
| title_short | Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles |
| title_sort | genome wide analysis of histone modifiers in tomato gaining an insight into their developmental roles |
| topic | <it>Solanum lycopersicum</it> Epigenetics Development |
| url | http://www.biomedcentral.com/1471-2164/14/57 |
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