Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
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.
Publication Types
["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]
MeSH Terms
["HeLa Cells", "Hep G2 Cells", "Humans", "Hydrogen Bonding", "Immunoprecipitation", "K562 Cells", "Nucleic Acid Conformation", "RNA", "RNA-Binding Proteins", "Transcriptome"]
Funding
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)
Linked Datasets (1)
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens160 data files
| File | Type | Size |
|---|---|---|
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 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_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| MC_DMS1_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| 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_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 MB |
| MC_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 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_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 MB |
| MC_DMS2_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 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_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 MB |
| MC_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 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_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| 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_NAI2_IP_S55_L008_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI2_IP_S55_L008_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_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 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_noDMS1_IP_S53_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_IP_S53_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_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| MC_noDMS2_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| 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_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 MB |
| MC_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 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_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| MC_noNAI1_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| 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_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 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_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noNAI2_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 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_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| MC_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| 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_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| MC_vitro1_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| 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_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| MC_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| 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_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 MB |
| MC_vitro2_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 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_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| 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_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 GB |
| MC_vivo1_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 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_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 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_Input_S2_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_Input_S2_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 |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
Analysis Pipelines (1)
GSE149767 eCLIP Data Processing
14 steps