Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Shatakshi Pandit, Yu Zhou, Lily Shiue, Gabriela Coutinho-Mansfield, Hairi Li, Jinsong Qiu, Jie Huang, Gene W Yeo, Manuel Ares, Xiang-Dong Fu
Molecular cell · 2013 · Vol. 50 (2) · pp. 223-35
Abstract
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins, SRSF1 (SF2/ASF) and SRSF2 (SC35), using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.
Linked datasets 2
Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing
Mus musculus
12 data files
| File | Type | Size |
|---|---|---|
| SRR765756_GSM1088390 | RNA-Seq | 1.2 GB |
| SRR765757_GSM1088391 | RNA-Seq | 1.3 GB |
| SRR765758 | RNA-Seq | 678.3 MB |
| SRR765758_GSM1088392 | RNA-Seq | 678.0 MB |
| SRR765759 | RNA-Seq | 3.4 GB |
| SRR765759_GSM1088392 | RNA-Seq | 3.4 GB |
| SRR765760 | RNA-Seq | 745.2 MB |
| SRR765760_GSM1088393 | RNA-Seq | 745.0 MB |
| SRR765761 | RNA-Seq | 3.5 GB |
| SRR765761_GSM1088393 | RNA-Seq | 3.5 GB |
| SRSF1.fastq.gz | RNA-Seq | 1.2 GB |
| SRSF2.fastq.gz | RNA-Seq | 1.3 GB |
Potentially related datasets 2
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
Analysis pipelines 2
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE44583 Microarray Data Processing geo_data_processing | Microarray | 4 | GSE44583 |
| GSE44591 CLIP-seq Data Processing geo_data_processing | CLIP-seq | 1 | GSE44591 |
Funding 8 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| R01 NS075449 | NINDS NIH HHS (United States) |
| R01 GM052872 | NIGMS NIH HHS (United States) |
| R01 GM049369 | NIGMS NIH HHS (United States) |
| HG004659 | NHGRI NIH HHS (United States) |
| R01 GM084317 | NIGMS NIH HHS (United States) |
| GM084317 | NIGMS NIH HHS (United States) |
| GM049369 | NIGMS NIH HHS (United States) |