Department of Basic Medicine, Medical College of Qinghai University, Xining 810016, China.
Genomics Proteomics Bioinformatics. 2013 Aug;11(4):247-52. doi: 10.1016/j.gpb.2013.05.006. Epub 2013 Jul 26.
Allele-specific expression refers to the preferential expression of one of the two alleles in a diploid genome, which has been thought largely attributable to the associated cis-element variation and allele-specific epigenetic modification patterns. Allele-specific expression may contribute to the heterosis (or hybrid vigor) effect in hybrid plants that are produced from crosses of closely-related species, subspecies and/or inbred lines. In this study, using Illumina high-throughput sequencing of maize transcriptomics, chromatic H3K27me3 histone modification and DNA methylation data, we developed a new computational framework to identify allele-specifically expressed genes by simultaneously tracking allele-specific gene expression patterns and the epigenetic modification landscape in the seedling tissues of hybrid maize. This approach relies on detecting nucleotide polymorphisms and any genomic structural variation between two parental genomes in order to distinguish paternally or maternally derived sequencing reads. This computational pipeline also incorporates a modified Chi-square test to statistically identify allele-specific gene expression and epigenetic modification based on the Poisson distribution.
等位基因特异性表达是指在二倍体基因组中优先表达两个等位基因中的一个，这主要归因于相关顺式元件变异和等位基因特异性表观遗传修饰模式。等位基因特异性表达可能有助于杂种植物的杂种优势（或杂种活力）效应，这些杂种植物是由亲缘关系密切的物种、亚种和/或自交系杂交产生的。在这项研究中，我们使用玉米转录组学的 Illumina 高通量测序、染色质 H3K27me3 组蛋白修饰和 DNA 甲基化数据，开发了一种新的计算框架，通过同时跟踪杂种玉米幼苗组织中的等位基因特异性基因表达模式和表观遗传修饰景观，来识别等位基因特异性表达的基因。该方法依赖于检测两个亲本基因组之间的核苷酸多态性和任何基因组结构变异，以区分来自父本或母本的测序reads。该计算流程还结合了一种改进的卡方检验，根据泊松分布在统计学上识别等位基因特异性基因表达和表观遗传修饰。
