Characterization of the Cannabis sativa glandular trichome epigenome
Abstract Background The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. The glandular trichomes of Cannabis s...
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BMC
2024-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05787-x |
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| author | Lee J. Conneely Bhavna Hurgobin Sophia Ng Muluneh Tamiru-Oli Mathew G. Lewsey |
| author_facet | Lee J. Conneely Bhavna Hurgobin Sophia Ng Muluneh Tamiru-Oli Mathew G. Lewsey |
| author_sort | Lee J. Conneely |
| collection | DOAJ |
| description | Abstract Background The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. The glandular trichomes of Cannabis sativa are an emerging model system that produce large quantities of cannabinoid and terpenoid specialised metabolites with known medicinal and commercial value. To address this lack of epigenomic data, we mapped H3K4 trimethylation, H3K56 acetylation, H3K27 trimethylation post-translational modifications and the histone variant H2A.Z, using chromatin immunoprecipitation, in C. sativa glandular trichomes, leaf, and stem tissues. Corresponding transcriptomic (RNA-seq) datasets were integrated, and tissue-specific analyses conducted to relate chromatin states to glandular trichome specific gene expression. Results The promoters of cannabinoid and terpenoid biosynthetic genes, specialised metabolite transporter genes, defence related genes, and starch and sucrose metabolism were enriched specifically in trichomes for histone marks H3K4me3 and H3K56ac, consistent with active transcription. We identified putative trichome-specific enhancer elements by identifying intergenic regions of H3K56ac enrichment, a histone mark that maintains enhancer accessibility, then associated these to putative target genes using the tissue specific gene transcriptomic data. Bi-valent chromatin loci specific to glandular trichomes, marked with H3K4 trimethylation and H3K27 trimethylation, were associated with genes of MAPK signalling pathways and plant specialised metabolism pathways, supporting recent hypotheses that implicate bi-valent chromatin in plant defence. The histone variant H2A.Z was largely found in intergenic regions and enriched in chromatin that contained genes involved in DNA homeostasis. Conclusion We report the first genome-wide histone post-translational modification maps for C. sativa glandular trichomes, and more broadly for glandular trichomes in plants. Our findings have implications in plant adaptation and stress responses and provide a basis for enhancer-mediated, targeted, gene transformation studies in plant glandular trichomes. |
| format | Article |
| id | doaj-art-717ce6354bda49b9ba121c8089e284ac |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-717ce6354bda49b9ba121c8089e284ac2025-02-02T12:15:35ZengBMCBMC Plant Biology1471-22292024-11-0124112010.1186/s12870-024-05787-xCharacterization of the Cannabis sativa glandular trichome epigenomeLee J. Conneely0Bhavna Hurgobin1Sophia Ng2Muluneh Tamiru-Oli3Mathew G. Lewsey4La Trobe Institute for Sustainable Agriculture and Food, La Trobe UniversityLa Trobe Institute for Sustainable Agriculture and Food, La Trobe UniversityLa Trobe Institute for Sustainable Agriculture and Food, La Trobe UniversityLa Trobe Institute for Sustainable Agriculture and Food, La Trobe UniversityLa Trobe Institute for Sustainable Agriculture and Food, La Trobe UniversityAbstract Background The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. The glandular trichomes of Cannabis sativa are an emerging model system that produce large quantities of cannabinoid and terpenoid specialised metabolites with known medicinal and commercial value. To address this lack of epigenomic data, we mapped H3K4 trimethylation, H3K56 acetylation, H3K27 trimethylation post-translational modifications and the histone variant H2A.Z, using chromatin immunoprecipitation, in C. sativa glandular trichomes, leaf, and stem tissues. Corresponding transcriptomic (RNA-seq) datasets were integrated, and tissue-specific analyses conducted to relate chromatin states to glandular trichome specific gene expression. Results The promoters of cannabinoid and terpenoid biosynthetic genes, specialised metabolite transporter genes, defence related genes, and starch and sucrose metabolism were enriched specifically in trichomes for histone marks H3K4me3 and H3K56ac, consistent with active transcription. We identified putative trichome-specific enhancer elements by identifying intergenic regions of H3K56ac enrichment, a histone mark that maintains enhancer accessibility, then associated these to putative target genes using the tissue specific gene transcriptomic data. Bi-valent chromatin loci specific to glandular trichomes, marked with H3K4 trimethylation and H3K27 trimethylation, were associated with genes of MAPK signalling pathways and plant specialised metabolism pathways, supporting recent hypotheses that implicate bi-valent chromatin in plant defence. The histone variant H2A.Z was largely found in intergenic regions and enriched in chromatin that contained genes involved in DNA homeostasis. Conclusion We report the first genome-wide histone post-translational modification maps for C. sativa glandular trichomes, and more broadly for glandular trichomes in plants. Our findings have implications in plant adaptation and stress responses and provide a basis for enhancer-mediated, targeted, gene transformation studies in plant glandular trichomes.https://doi.org/10.1186/s12870-024-05787-xCannabis sativaGlandular trichomesSpecialised metabolismMultiomicsH3K4me3H3K27me3 |
| spellingShingle | Lee J. Conneely Bhavna Hurgobin Sophia Ng Muluneh Tamiru-Oli Mathew G. Lewsey Characterization of the Cannabis sativa glandular trichome epigenome BMC Plant Biology Cannabis sativa Glandular trichomes Specialised metabolism Multiomics H3K4me3 H3K27me3 |
| title | Characterization of the Cannabis sativa glandular trichome epigenome |
| title_full | Characterization of the Cannabis sativa glandular trichome epigenome |
| title_fullStr | Characterization of the Cannabis sativa glandular trichome epigenome |
| title_full_unstemmed | Characterization of the Cannabis sativa glandular trichome epigenome |
| title_short | Characterization of the Cannabis sativa glandular trichome epigenome |
| title_sort | characterization of the cannabis sativa glandular trichome epigenome |
| topic | Cannabis sativa Glandular trichomes Specialised metabolism Multiomics H3K4me3 H3K27me3 |
| url | https://doi.org/10.1186/s12870-024-05787-x |
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