The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation
Abstract
:1. Introduction
2. Results
2.1. Histone Mark H3K9ac on SlyDES, SlyDOX1, SlyLoxD, and SlyWRKY75 Genes in Tomato Plants’ Early Response to B. cinerea
2.2. Histone Marks H3K9ac and H3K4me3 on SlyDES, SlyDOX1, SlyLoxD, and SlyWRKY75 Genes in Tomato Plants Infected by P. syringae
2.3. Presence of RNAPII in SlyDES, SlyDOX1, SlyLoxD, and SlyWRKY75 in Response to B. cinerea and P. syringae
2.4. Epigenetic Marks H3K9ac and H3K4me3 and the Presence of RNAPII at the SlyWRKY75 Intron in Response to B. cinerea or P. syringae
2.5. Analysis of SlyWRKY75 Transcript Processing in Response to B. cinerea or P. syringae
2.6. Epigenetic Marks H3K9ac and H3K4me3 and Presence of RNAPII in the Sly-miR1127-3p Structural Gene in Response to B. cinerea and P. syringae
3. Discussion
4. Materials and Methods
4.1. S. lycopersicum Growth Conditions
4.2. B. cinerea Bioassay
4.3. P. syringae Bioassay
4.4. Gene Expression Quantification by RT-qPCR
4.5. miRNA Assay
4.6. Chromatin Isolation and Immunoprecipitation Protocol
4.7. Data Interpretation and Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Region | B. cinerea | P. syringae | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Expression 1 | H3K9ac | H3K4me3 1 | RNAPII | Expression | H3K9ac | H3K4me3 | RNAPII | |||
SlyDES | Promoter | +++ | ↑↑↑ | ↑ | ↑↑↑ | ++ | ||||
TSS | ↑↑↑ | ↑↑ | ↑↑ | ↑ | ↑ | |||||
Exon 2 (end of CDS) | ↑↑↑ | ↑↑ | ↑↑↑ | |||||||
SlyDOX1 | Promoter | +++ | ↑↑ | ↑ | ↑ | ++ | ↑ | |||
TSS | ↑↑ | ↑↑ | ↑ | ↑ | ↑ | |||||
Exon 1 (start of CDS) | ↑ | ↑↑ | ↑ | ↑ | ||||||
Exon 10 (end of CDS) | ↑↑ | ↑↑ | ↑ | ↑ | ||||||
SlyLoxD | Promoter | ++ | ↑ | ↑↑ | + | ↑ | ||||
TSS | ↑↑ | ↑ | ||||||||
Exon 1 | ↑↑ | ↑↑ | ↑ | ↑ | ||||||
Exon 8 (3’-UTR) | ↑ | ↑ | ↑ | ↑↑ | ||||||
SlyWRKY75 2 | TSS | ++ | ↑↑ | ↑ | ↑↑ | ++ | ↑↑ | ↑↑ | ↑↑ | |
Exon 1 | ↑ | ↑↑ | ↑ | ↑↑ | ↑↑↑ | |||||
Intron | miRNA binding region | ↑↑ | ↑↑ | ↑↑ | ↑ | ↑↑↑ | ||||
Region 1 | ↑↑ | ↑↑ | ↑↑ | ↑↑ | ↑↑↑ | |||||
Region 2 | ↑↑ | ↑↑ | ↑↑ | ↑↑↑ | ↑↑ | ↑↑↑ | ||||
Region 3 | ↑↑ | ↑↑ | ↑↑ | ↑↑↑ | ↑↑ | ↑↑↑ | ||||
Exon 2 (3’-UTR) | ↑ | ↑↑ | ↑ | ↑↑↑ | ||||||
miR1127-3p 2 | Promoter | − | ↑ | ↓ | ||||||
TSS | ↓ | |||||||||
3’ gene and intergenic region |
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Crespo-Salvador, Ó.; Sánchez-Giménez, L.; López-Galiano, M.J.; Fernández-Crespo, E.; Scalschi, L.; García-Robles, I.; Rausell, C.; Real, M.D.; González-Bosch, C. The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation. Plants 2020, 9, 300. https://doi.org/10.3390/plants9030300
Crespo-Salvador Ó, Sánchez-Giménez L, López-Galiano MJ, Fernández-Crespo E, Scalschi L, García-Robles I, Rausell C, Real MD, González-Bosch C. The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation. Plants. 2020; 9(3):300. https://doi.org/10.3390/plants9030300
Chicago/Turabian StyleCrespo-Salvador, Óscar, Lorena Sánchez-Giménez, Mª José López-Galiano, Emma Fernández-Crespo, Loredana Scalschi, Inmaculada García-Robles, Carolina Rausell, M Dolores Real, and Carmen González-Bosch. 2020. "The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation" Plants 9, no. 3: 300. https://doi.org/10.3390/plants9030300