Wang Xiangfeng, Elling Axel A, Li Xueyong, Li Ning, Peng Zhiyu, He Guangming, Sun Hui, Qi Yijun, Liu X Shirley, Deng Xing Wang
Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China.
Plant Cell. 2009 Apr;21(4):1053-69. doi: 10.1105/tpc.109.065714. Epub 2009 Apr 17.
Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.
玉米（Zea mays）拥有异常复杂的基因组，在表观遗传学和进化方面都有着丰富的历史。我们报告了玉米地上部和根部代表性表观遗传修饰的基因组图谱及其与mRNA和小RNA（smRNA）转录组的关系。基因和转座元件之间的表观遗传模式差异巨大，两种抑制性标记（H3K27me3和DNA甲基化）通常相互排斥。我们发现了典型微RNA（miRNA）和内源性小干扰RNA（siRNA）的器官特异性分布，这表明它们的组织特异性生物合成。此外，我们观察到，mop1水平的降低会导致24核苷酸siRNA相对于21核苷酸miRNA以组织特异性方式随之减少。一组22核苷酸的siRNA可能源自长发夹双链RNA，并优先靶向基因编码区。此外，一类类似miRNA的smRNA，其推定前体可形成短发夹，可能会反式靶向基因。总之，我们的数据对玉米表观基因组及其与mRNA和smRNA转录组的关系进行了批判性分析。
