Renal Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Mol Cell Biol. 2012 Apr;32(8):1468-82. doi: 10.1128/MCB.06536-11. Epub 2012 Feb 21.
Tissue-specific alternative splicing is achieved through the coordinated assembly of RNA binding proteins at specific sites to enhance or silence splicing at nearby splice sites. We used high-throughput sequencing (RNA-Seq) to investigate the complete spectrum of alternative splicing events that are regulated by the epithelium-specific splicing regulatory proteins ESRP1 and ESRP2. We also combined this analysis with direct RNA sequencing (DRS) to reveal ESRP-mediated regulation of alternative polyadenylation. To define binding motifs that mediate direct regulation of splicing and polyadenylation by ESRP, SELEX-Seq analysis was performed, coupling traditional SELEX with high-throughput sequencing. Identification and scoring of high-affinity ESRP1 binding motifs within ESRP target genes allowed the generation of RNA maps that define the position-dependent activity of the ESRPs in regulating cassette exons and alternative 3' ends. These extensive analyses provide a comprehensive picture of the functions of the ESRPs in an epithelial posttranscriptional gene expression program.
组织特异性可变剪接是通过 RNA 结合蛋白在特定位置的协调组装来实现的，以增强或沉默附近剪接位点的剪接。我们使用高通量测序（RNA-Seq）来研究受上皮细胞特异性剪接调控蛋白 ESRP1 和 ESRP2 调控的完整可变剪接事件谱。我们还将此分析与直接 RNA 测序（DRS）相结合，揭示了 ESRP 介导的可变多聚腺苷酸化调控。为了确定介导 ESRP 对剪接和多聚腺苷酸化的直接调控的结合基序，进行了 SELEX-Seq 分析，将传统 SELEX 与高通量测序相结合。在 ESRP 靶基因内鉴定和评分高亲和力 ESRP1 结合基序，允许生成 RNA 图谱，该图谱定义了 ESRPs 在调节盒外显子和替代 3' 末端中的位置依赖性活性。这些广泛的分析提供了 ESRPs 在上皮细胞转录后基因表达程序中的功能的全面描述。
