title: Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation.
abstract: Epigenetic modifications are highlighted for their great importance in regulating plant development, but their function associated with single-cell differentiation remains undetermined. Here, we used the cotton fibre, which is the epidermal hair on the cotton ovule, as a model to investigate the regulatory role of DNA methylation in cell differentiation. The level of CHH (H = A, T, or C) DNA methylation level was found to increase during fibre development, accompanied by a decrease in RNA-directed DNA methylation (RdDM). Examination of nucleosome positioning revealed a gradual transition from euchromatin to heterochromatin for chromatin dynamics in developing fibres, which could shape the DNA methylation landscape. The observed increase in DNA methylation in fibres, compared with other ovule tissue, was demonstrated to be mediated predominantly by an active H3K9me2-dependent pathway rather than the RdDM pathway, which was inactive. Furthermore, integrated multi-omics analyses revealed that dynamic DNA methylation played a role in the regulation of lipid biosynthesis and spatio-temporal modulation of reactive oxygen species during fibre differentiation. Our study illustrates two divergent pathways mediating a continuous increase of DNA methylation and also sheds further light on the epigenetic basis for single-cell differentiation in plants. These data and analyses are made available to the wider research community through a comprehensive web portal.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Maojun
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Tu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Sitao
authors.initials: S
authors.lastname: Zhu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Daojun
authors.initials: D
authors.lastname: Yuan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China xlzhang@mail.hzau.edu.cn.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D032561:Cotton Fiber; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D022041:Euchromatin / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D015723:Gene Library; D017343:Genes, Plant; D003368:Gossypium / Q000166:cytology / Q000235:genetics*; D006570:Heterochromatin / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism
chemical_list: D022041:Euchromatin; D006570:Heterochromatin; D009707:Nucleosomes