Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing
| Autor: | Karine Amirikian, Shihao Shen, Yi Xing, Russ P. Carstens, Juw Won Park, Kimberly Dittmar, Ji Wan, Peng Jiang |
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| Rok vydání: | 2012 |
| Předmět: |
Exonic splicing enhancer
RNA-binding protein Computational biology Biology Epithelium Splicing factor Humans Nucleotide Motifs Molecular Biology Genetics Binding Sites Base Sequence Genome Human Sequence Analysis RNA Alternative splicing Intron RNA-Binding Proteins Articles Cell Biology Post-transcriptional modification Alternative Splicing Epithelial Splicing Regulatory Protein 1 Organ Specificity RNA splicing RNA Splice Sites Genome-Wide Association Study |
| Zdroj: | Molecular and Cellular Biology. 32:1468-1482 |
| ISSN: | 1098-5549 |
| DOI: | 10.1128/mcb.06536-11 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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