Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Linked Datasets (3)
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion
Homo sapiensSystematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [RNA-seq]
Homo sapiens30 data files
| File | Type | Size |
|---|---|---|
| shNT_1_R1.fastq.gz | RNA-Seq | 5.0 GB |
| shNT_1_R1.fastq.gz | RNA-Seq | 5.0 GB |
| shNT_2_R1.fastq.gz | RNA-Seq | 5.2 GB |
| shNT_2_R1.fastq.gz | RNA-Seq | 5.2 GB |
| shNT_3_R1.fastq.gz | RNA-Seq | 6.3 GB |
| shNT_3_R1.fastq.gz | RNA-Seq | 6.3 GB |
| shRTCA_1_R1.fastq.gz | RNA-Seq | 5.3 GB |
| shRTCA_1_R1.fastq.gz | RNA-Seq | 5.3 GB |
| shRTCA_2_R1.fastq.gz | RNA-Seq | 4.7 GB |
| shRTCA_2_R1.fastq.gz | RNA-Seq | 4.7 GB |
| shRTCA_3_R1.fastq.gz | RNA-Seq | 5.0 GB |
| shRTCA_3_R1.fastq.gz | RNA-Seq | 5.0 GB |
| shSCAF8_1_R1.fastq.gz | RNA-Seq | 4.9 GB |
| shSCAF8_1_R1.fastq.gz | RNA-Seq | 4.9 GB |
| shSCAF8_2_R1.fastq.gz | RNA-Seq | 5.3 GB |
| shSCAF8_2_R1.fastq.gz | RNA-Seq | 5.3 GB |
| shSCAF8_3_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shSCAF8_3_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shSTAU2_1_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shSTAU2_1_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shSTAU2_2_R1.fastq.gz | RNA-Seq | 4.6 GB |
| shSTAU2_2_R1.fastq.gz | RNA-Seq | 4.6 GB |
| shSTAU2_3_R1.fastq.gz | RNA-Seq | 4.7 GB |
| shSTAU2_3_R1.fastq.gz | RNA-Seq | 4.7 GB |
| shTRNAU1AP_1_R1.fastq.gz | RNA-Seq | 5.6 GB |
| shTRNAU1AP_1_R1.fastq.gz | RNA-Seq | 5.6 GB |
| shTRNAU1AP_2_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shTRNAU1AP_2_R1.fastq.gz | RNA-Seq | 4.8 GB |
| shTRNAU1AP_3_R1.fastq.gz | RNA-Seq | 5.6 GB |
| shTRNAU1AP_3_R1.fastq.gz | RNA-Seq | 5.6 GB |
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]
Homo sapiens40 data files
| File | Type | Size |
|---|---|---|
| FLAG_IN1.fastq.gz | RIP-Seq | 928.9 MB |
| FLAG_IN1.fastq.gz | RIP-Seq | 928.9 MB |
| FLAG_IN2.fastq.gz | RIP-Seq | 1.0 GB |
| FLAG_IN2.fastq.gz | RIP-Seq | 1.0 GB |
| FLAG_IP1.fastq.gz | RIP-Seq | 864.1 MB |
| FLAG_IP1.fastq.gz | RIP-Seq | 864.1 MB |
| FLAG_IP2.fastq.gz | RIP-Seq | 802.7 MB |
| FLAG_IP2.fastq.gz | RIP-Seq | 802.7 MB |
| RTCA_IN1.fastq.gz | RIP-Seq | 824.8 MB |
| RTCA_IN1.fastq.gz | RIP-Seq | 824.8 MB |
| RTCA_IN2.fastq.gz | RIP-Seq | 808.7 MB |
| RTCA_IN2.fastq.gz | RIP-Seq | 808.7 MB |
| RTCA_IP1.fastq.gz | RIP-Seq | 816.4 MB |
| RTCA_IP1.fastq.gz | RIP-Seq | 816.4 MB |
| RTCA_IP2.fastq.gz | RIP-Seq | 858.7 MB |
| RTCA_IP2.fastq.gz | RIP-Seq | 858.7 MB |
| SCAF8_IN1.fastq.gz | RIP-Seq | 746.9 MB |
| SCAF8_IN1.fastq.gz | RIP-Seq | 746.9 MB |
| SCAF8_IN2.fastq.gz | RIP-Seq | 882.8 MB |
| SCAF8_IN2.fastq.gz | RIP-Seq | 882.8 MB |
| SCAF8_IP1.fastq.gz | RIP-Seq | 782.9 MB |
| SCAF8_IP1.fastq.gz | RIP-Seq | 782.9 MB |
| SCAF8_IP2.fastq.gz | RIP-Seq | 852.6 MB |
| SCAF8_IP2.fastq.gz | RIP-Seq | 852.6 MB |
| STAU2_IN1.fastq.gz | RIP-Seq | 805.7 MB |
| STAU2_IN1.fastq.gz | RIP-Seq | 805.7 MB |
| STAU2_IN2.fastq.gz | RIP-Seq | 902.6 MB |
| STAU2_IN2.fastq.gz | RIP-Seq | 902.6 MB |
| STAU2_IP1.fastq.gz | RIP-Seq | 925.0 MB |
| STAU2_IP1.fastq.gz | RIP-Seq | 925.0 MB |
| STAU2_IP2.fastq.gz | RIP-Seq | 876.9 MB |
| STAU2_IP2.fastq.gz | RIP-Seq | 876.9 MB |
| TRNAU1AP_IN1.fastq.gz | RIP-Seq | 652.9 MB |
| TRNAU1AP_IN1.fastq.gz | RIP-Seq | 652.9 MB |
| TRNAU1AP_IN2.fastq.gz | RIP-Seq | 493.3 MB |
| TRNAU1AP_IN2.fastq.gz | RIP-Seq | 493.3 MB |
| TRNAU1AP_IP1.fastq.gz | RIP-Seq | 514.1 MB |
| TRNAU1AP_IP1.fastq.gz | RIP-Seq | 514.1 MB |
| TRNAU1AP_IP2.fastq.gz | RIP-Seq | 819.3 MB |
| TRNAU1AP_IP2.fastq.gz | RIP-Seq | 819.3 MB |
Potentially Related Datasets (1)
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.