Nucl Acids Res:华中农业大学张献龙研究组绘成棉花纤维发育过程中
2016年3月28日，国际知名核酸研究期刊《Nucleic Acids Research》杂志在线发表华中农业大学作物遗传改良国家重点实验室棉花团队关于棉花纤维表观遗传研究取得新进展，研究题为Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation的研究利用多组学数据揭示了棉花纤维发育的表观遗传基础。本研究首次绘制了棉花纤维发育过程中表观修饰的动态图谱，对进一步研究植物单细胞分化具有重要意义。团队博士研究生王茂军为论文第一作者，张献龙教授为通讯作者。
表观遗传修饰在调控植物发育过程中发挥着重要作用，但是人们对其在单细胞分化中的功能认识很少。该团队前期题为“Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.)”的研究表明，长链非编码RNA在棉花纤维发育过程中发挥着重要作用。为了进一步揭示表观修饰的重要作用，本研究绘制了棉花纤维发育的动态DNA甲基化图谱。研究发现：在棉花纤维发育过程中，DNA甲基化的比例会逐渐升高，呈现出与RNA介导的DNA甲基化相反的趋势。核小体定位分析表明发育中的纤维细胞核不断异染色质化，这可能与DNA甲基化的增加相关。相对于胚珠，绝大部分纤维特异的DNA甲基化是由H3K9me2依赖的途径建立的，与RNA介导的DNA甲基化不相关。通过分析四倍体棉花At和Dt亚组同源基因甲基化和表达量之间的关系，推测纤维发育过程中不同亚组基因的差异表观修饰可能会是基因偏向性表达的原因之一。
原文链接：
Multi-omics maps of cotton fibre reveal epiGENEtic basis for staged single-cell differentiation
原文摘要：
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.
作者：张献龙
