Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing
Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing
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DOI：
10.1128/mcb.06536-11
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发表时间：
2012-04-01
影响因子：
5.3
通讯作者：
Carstens, Russell P.
中科院分区：
文献类型：
--
作者：
Dittmar, Kimberly A.;Jiang, Peng;Carstens, Russell P.
组织特异性选择性剪接是通过在特定位置协调组装RNA结合蛋白来增强或抑制附近剪接位点的剪接而实现的。我们使用高通量测序(RNA-Seq)来研究由上皮特异性剪接调控蛋白ESRP1和ESRP2调控的选择性剪接事件的完整谱。我们还将这一分析与RNA直接测序(DRS)相结合，以揭示ESRP介导的选择性多聚腺苷基化的调节。为了确定介导ESRP直接调控剪接和聚腺苷酸化的结合基序，进行了SELEX-SEQ分析，将传统的SELEX与高通量测序相结合。对ESRP靶基因中高亲和力的ESRP1结合基序的鉴定和评分允许生成RNA图谱，该图谱定义了ESRP在调节盒外显子和替代3‘端中的位置依赖性活性。这些广泛的分析为ESRPs在上皮转录后基因表达程序中的功能提供了一个全面的图景。
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.