Analysis of a dominant epigenetic modifier of pericarp color1 (p1) gene of maize

研究者先前已经表征了玉米p1（果皮颜色1）基因等位基因的表达模式和基因结构。P1是一种myb类型的转录因子，控制红色类黄酮色素（称为phlobaphenes）的生物合成。以前的研究结果表明，等位基因的表达在p1基因座是一个功能的基因结构和基因组织，这是进一步调控的表观遗传机制。 研究人员现在已经描述了一种名为Ufo 1（橙色不稳定因子1）的主要修饰剂。 在不存在Ufo 1的情况下，P1-wr（白色果皮红色穗轴颖片）等位基因的植物产生具有无色籽粒果皮和红色穗轴的穗，并且该表型高度稳定。在Ufo 1存在下，P1-wr赋予增强的籽粒果皮、穗轴和植物色素沉着。 初步的表达研究表明，色素沉着的增益与增加的稳态水平的p1转录本，这是与减少DNA甲基化的启动子和编码序列的P1-wr。 进一步的实验将通过p1等位基因的瞬时DNA甲基化变化研究Ufo 1诱导的程序性表达谱的失调。 具体而言，1）使用亚硫酸氢盐测序方法，该项目将鉴定在Ufo 1存在下p1序列中DNA甲基化修饰的特定类型和位置，2）从Ufo 1与ufo 1基因型RNA的微阵列分析中鉴定的基因将进一步测试其表达和功能，3）克隆Ufo 1基因，该研究项目将开始开发植物种群，以在10号染色体短臂上已知的原始位置内精细绘制Ufo 1因子。 从长远来看，这项研究将导致识别的分子标记和机制，可能调节稳定的转基因和天然等位基因。研究生和本科生将执行本项目的大部分研究。 该项目将提供表观遗传学和功能基因组学方面的培训机会。

Chopra AbstractThe investigator has previously characterized the expression pattern and gene structure of alleles of the maize p1 (pericarp color1) gene. P1 is a myb type of transcription factor and controls the biosynthesis of red flavonoid pigments called phlobaphenes. Previous findings suggest that allelic expression at the p1 locus is a function of the gene structure and gene organization, which is further regulated by epigenetic mechanisms. The investigator has now characterized a dominant modifier called Ufo1 (Unstable factor for orange1). In the absence of Ufo1, plants of P1-wr (white pericarp & red cob glumes) allele produce ears with colorless kernel pericarp and red cobs and this phenotype is highly stable. In the presence of Ufo1, the P1-wr confers variably enhanced kernel pericarp, cob and plant pigmentation. Preliminary expression studies demonstrate that the gain of pigmentation is associated with increased steady state levels of p1 transcript that is correlated with decrease in DNA methylation of promoter and coding sequence of the P1-wr. Further experiments will investigate Ufo1 induced de-regulation of a well-programmed expression profile via transient DNA methylation changes of p1 alleles. Specifically, 1) using bisulfite sequencing methods, this project will identify specific type(s) and position(s) of DNA methylation modifications in the p1 sequence in the presence of Ufo1, 2) genes identified from the microarray analysis of Ufo1 versus ufo1 genotype RNA will be further tested for their expression and functionality and 3) to clone the Ufo1 gene, the research project will begin to develop plant populations to fine map the Ufo1 factor within the known crude position on the short arm of chromosome 10. In the longer run, this study will lead to the identification of molecular marks and mechanisms that may regulate stability of transgenes and natural alleles. Graduate students and undergraduates students will perform the majority of the research on this project. This project will provide training opportunities in epigenetics, as well as in functional genomics.