Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
Meredith Corley, Ryan A Flynn, Byron Lee, Steven M Blue, Howard Y Chang, Gene W Yeo
Molecular cell · 2020 · Vol. 80 (5) · pp. 903-914.e8
Abstract
Discovering the interaction mechanism and location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four human cell lines to identify transcriptome-wide footprints (fSHAPE) on RNA. Structural analyses indicate that fSHAPE precisely detects nucleobases that hydrogen bond with protein. We demonstrate that fSHAPE patterns predict binding sites of known RBPs, such as iron response elements in both known loci and previously unknown loci in CDC34, SLC2A4RG, COASY, and H19. Furthermore, by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs, we interrogate specific RNA-protein complexes, such as histone stem-loop elements and their nucleotides that hydrogen bond with stem-loop-binding proteins. Together, these technologies greatly expand our ability to study and understand specific cellular RNA interactions in RNA-protein complexes.
Linked datasets 1
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens
81 data files
| File | Type | Size |
|---|---|---|
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| MC_DMS1_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| MC_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 MB |
| MC_DMS2_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 MB |
| MC_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 MB |
| MC_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI2_IP_S55_L008_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noDMS1_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_IP_S53_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS2_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| MC_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 MB |
| MC_noNAI1_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| MC_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_noNAI2_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| MC_vitro1_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| MC_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| MC_vitro2_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 MB |
| MC_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_vivo1_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 GB |
| MC_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_Input_S2_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| SRR11682352_GSM4512071 | OTHER | 16.1 GB |
| SRR11682353_GSM4512072 | OTHER | 13.2 GB |
| SRR11682354_GSM4512073 | OTHER | 16.7 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
| SRR11682355_GSM4512074 | OTHER | 16.2 GB |
| SRR11682356_GSM4512075 | OTHER | 12.3 GB |
| SRR11682357_GSM4512076 | OTHER | 10.7 GB |
| SRR11682358_GSM4512077 | OTHER | 13.3 GB |
| SRR11682359_GSM4512078 | OTHER | 13.5 GB |
| SRR11682360_GSM4512079 | OTHER | 13.5 GB |
| SRR11682361_GSM4512080 | OTHER | 12.9 GB |
| SRR11682362_GSM4512081 | OTHER | 12.5 GB |
| SRR11682363_GSM4512082 | OTHER | 4.8 GB |
| SRR11682364_GSM4512083 | OTHER | 1.0 GB |
| SRR11682365_GSM4512084 | OTHER | 811.0 MB |
| SRR11682366_GSM4512085 | OTHER | 1.0 GB |
| SRR11682367_GSM4512086 | OTHER | 720.0 MB |
| SRR11682368_GSM4512087 | OTHER | 813.0 MB |
| SRR11682369_GSM4512088 | OTHER | 932.0 MB |
| SRR11682370_GSM4512089 | OTHER | 821.0 MB |
| SRR11682371_GSM4512090 | OTHER | 1017.0 MB |
| SRR11682372_GSM4512091 | OTHER | 1.5 GB |
| SRR11682373_GSM4512092 | OTHER | 937.0 MB |
| SRR11682374_GSM4512093 | OTHER | 1.3 GB |
| SRR11682375_GSM4512094 | OTHER | 1.2 GB |
| SRR11682376_GSM4512095 | OTHER | 1.2 GB |
| SRR11682377_GSM4512096 | OTHER | 1.2 GB |
| SRR11682378_GSM4512097 | OTHER | 1.2 GB |
| SRR11682379_GSM4512098 | OTHER | 1.0 GB |
| SRR11682380_GSM4512099 | OTHER | 1.6 GB |
| SRR11682381_GSM4512100 | OTHER | 1.2 GB |
| SRR11682382_GSM4512101 | OTHER | 897.0 MB |
| SRR11682383_GSM4512102 | OTHER | 1.5 GB |
| SRR11682384_GSM4512103 | OTHER | 1.7 GB |
| SRR11682385_GSM4512104 | OTHER | 1022.0 MB |
| SRR12668784_GSM4795047 | OTHER | 5.3 GB |
| SRR12668785_GSM4795048 | OTHER | 7.9 GB |
| SRR12668786_GSM4795049 | OTHER | 5.8 GB |
| SRR12668787_GSM4795050 | OTHER | 6.7 GB |
| SRR12668788_GSM4795051 | OTHER | 6.6 GB |
| SRR12668789_GSM4795052 | OTHER | 5.1 GB |
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.
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE149767 eCLIP Data Processing geo_data_processing | eCLIP | 14 | GSE149767 |
Funding 8 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |
| Howard Hughes Medical Institute (United States) | |
| R01 HL137223 | NHLBI NIH HHS (United States) |
| R01 HL137219 | NHLBI NIH HHS (United States) |
| R35 CA209919 | NCI NIH HHS (United States) |
| R01 HD085902 | NICHD NIH HHS (United States) |
| R01 HG004361 | NHGRI NIH HHS (United States) |