ratio-based analysis of differential mrna processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarrayratio-based微分mrna分析处理和表达一个聚腺苷酸化因子突变pcfs4使用拟南芥花砖微阵列.pdfVIP

Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray 1,2. 2. 1,2 2 2 1 Jianti Zheng , Denghui Xing , Xiaohui Wu , Yingjia Shen , Diana M. Kroll , Guoli Ji *, Qingshun Quinn Li1,2* 1 Department of Automation, Xiamen University, Xiamen, Fujian, China, 2 Department of Botany, Miami University, Oxford, Ohio, United States of America Abstract Background: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development. Methodology/Principal Findings: To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data— variations caused by differential probe affinity—was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of th