PDF(Pubmed)
Abstract：
BACKGROUND: DNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance.
RESULTS: In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance.
CONCLUSIONS: In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.
RESULTS: In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance.
CONCLUSIONS: In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.
摘要：
背景：DNA甲基化有助于核基因表达的表观遗传调控，与植物生长有关，发展,和应激反应。令人信服的证据表明，长链非编码RNA（lncRNA）调节DNA甲基化。先前的遗传和生理证据表明，lncRNA-CRIR1在木薯植物对冷胁迫的反应中起积极作用。然而,目前尚不清楚全球DNA甲基化是否随着CRIR1促进的耐寒性而发生变化。
结果：在这项研究中，我们对DNA甲基化和转录组谱进行了综合比较分析,以揭示CRIR1过表达后的基因表达和表观遗传动力学.与野生型植物相比,CRIR1过表达的植物在超过37,000个基因组区域中获得了DNA甲基化，在约16,000个基因组区域中丢失了DNA甲基化，表明CRIR1过表达后DNA甲基化的整体降低。DNA甲基化的下降与DNA甲基化酶/去甲基酶基因的表达降低/增加无关。但与一些转录因子的转录本增加有关，叶绿素代谢和光合作用相关基因，这可能有助于CRIR1促进耐寒性。
结论：总之，本研究整合了第一组转录组和表观基因组数据，以揭示CRIR1过表达后的基因表达和表观遗传动力学，随着几个TFs的识别，叶绿素代谢和光合作用相关基因可能参与CRIR1促进的耐寒性。因此,我们的研究为系统研究植物冷胁迫响应的分子见解提供了有价值的数据。
结果：在这项研究中，我们对DNA甲基化和转录组谱进行了综合比较分析,以揭示CRIR1过表达后的基因表达和表观遗传动力学.与野生型植物相比,CRIR1过表达的植物在超过37,000个基因组区域中获得了DNA甲基化，在约16,000个基因组区域中丢失了DNA甲基化，表明CRIR1过表达后DNA甲基化的整体降低。DNA甲基化的下降与DNA甲基化酶/去甲基酶基因的表达降低/增加无关。但与一些转录因子的转录本增加有关，叶绿素代谢和光合作用相关基因，这可能有助于CRIR1促进耐寒性。
结论：总之，本研究整合了第一组转录组和表观基因组数据，以揭示CRIR1过表达后的基因表达和表观遗传动力学，随着几个TFs的识别，叶绿素代谢和光合作用相关基因可能参与CRIR1促进的耐寒性。因此,我们的研究为系统研究植物冷胁迫响应的分子见解提供了有价值的数据。
