Zhao Hainan, Zhu Xiaobiao, Wang Kai, Gent Jonathan I, Zhang Wenli, Dawe R Kelly, Jiang Jiming
Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706.
Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
G3 (Bethesda). 2015 Nov 12;6(1):183-92. doi: 10.1534/g3.115.022764.
Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize.
着丝粒由CENH3（组蛋白H3的一种变体）的存在来定义。大多数植物物种的着丝粒仅包含高度重复的DNA序列，这阻碍了对着丝粒染色质结构和功能的研究。几个玉米着丝粒已近乎完全测序，为植物着丝粒的基因组和表观基因组研究提供了一个基于序列的平台。在此，我们报告了玉米基因组中CENH3核小体的高分辨率图谱。尽管CENH3核小体平均间隔约190 bp，但占据CentC（一个156 bp的着丝粒卫星重复序列）的CENH3核小体显示出与CentC单体对齐的清晰定位。玉米着丝粒包含交替的富含CENH3和缺乏CENH3的亚结构域，分别占着丝粒的87%和13%。在着丝粒中鉴定出了许多注释基因，包括11个仅位于缺乏CENH3的亚结构域中的活性基因。在玉米着丝粒中检测到的常染色质组蛋白修饰标记，包括H3K4me3、H3K36me3和H3K9ac，主要与活性基因相关联。有趣的是，相对于着丝粒周围区域，玉米着丝粒中异染色质组蛋白修饰标记H3K27me2的水平也较低。我们得出结论，H3K27me2和三种常染色质组蛋白修饰都不太可能作为玉米着丝粒身份的功能重要表观遗传标记。
