High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Qishan Liang, Tao Yu, Eric Kofman, Pratibha Jagannatha, Kevin Rhine, Brian A Yee, Kevin D Corbett, Gene W Yeo
Nature communications · 2024 · Vol. 15 (1) · pp. 7067
Abstract
RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE (IN situ Sensitive Capture of RNA-protein Interactions in Biological Environments), circumventing the challenges through in situ RNA labeling by precisely directing a purified APOBEC1-nanobody fusion to the RBP of interest. This method enables highly specific RNA-binding site identification across a diverse range of fixed biological samples such as HEK293T cells and mouse brain tissue and accurately identifies the canonical binding motifs of RBFOX2 (UGCAUG) and TDP-43 (UGUGUG) in native cellular environments. Applicable to any RBP with available primary antibodies, INSCRIBE enables sensitive capture of RBP-RNA interactions from ultra-low input equivalent to ~5 cells. The robust, versatile, and sensitive INSCRIBE workflow is particularly beneficial for precious tissues such as clinical samples, empowering the exploration of genuine RBP-RNA interactions in RNA-related disease contexts.
Linked datasets 10
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| 100pg_34_S12_L001_R1_001.fastq.gz | RNA-Seq | 1.9 GB |
| 100pg_35_S13_L001_R1_001.fastq.gz | RNA-Seq | 1.8 GB |
| 100pg_36_S14_L001_R1_001.fastq.gz | RNA-Seq | 1.6 GB |
| 1ng_19_S1_L001_R1_001.fastq.gz | RNA-Seq | 1.8 GB |
| 1ng_20_S2_L001_R1_001.fastq.gz | RNA-Seq | 1.8 GB |
| 1ng_33_S4_L001_R1_001.fastq.gz | RNA-Seq | 2.0 GB |
| 1ng_34_S5_L001_R1_001.fastq.gz | RNA-Seq | 1.8 GB |
| 1ng_35_S6_L001_R1_001.fastq.gz | RNA-Seq | 2.0 GB |
| 1ng_36_S7_L001_R1_001.fastq.gz | RNA-Seq | 2.0 GB |
| SRR26918586.lite | RNA-Seq | 1.9 GB |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]"
Homo sapiens
4 data files
| File | Type | Size |
|---|---|---|
| m64278e_230504_212705.reads.bam | RNA-Seq | 6.7 GB |
| m64278e_230504_212705.reads.bam | RNA-Seq | 6.7 GB |
| m64278e_230505_212742.reads.bam | RNA-Seq | 7.4 GB |
| m64278e_230505_212742.reads.bam | RNA-Seq | 7.4 GB |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells
Mus musculus
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| APOBEC1_rep2.aligned.bam | OTHER | 916.8 MB |
| APOBEC1_rep2.aligned.bam | OTHER | 916.8 MB |
| APOBEC1_rep3.aligned.bam | OTHER | 1.4 GB |
| APOBEC1_rep3.aligned.bam | OTHER | 1.4 GB |
| BUFFER_rep1.aligned.bam | OTHER | 1.4 GB |
| BUFFER_rep1.aligned.bam | OTHER | 1.4 GB |
| BUFFER_rep2.aligned.bam | OTHER | 1.4 GB |
| BUFFER_rep2.aligned.bam | OTHER | 1.4 GB |
| RBFOX2_rep1.aligned.bam | OTHER | 1.4 GB |
| RBFOX2_rep2.aligned.bam | OTHER | 1.5 GB |
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
Homo sapiens
Expanded repertoire for RNA-editing-based detection for RNA binding protein interactions (3)
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| Hugo-E1_S31_L002_R1_001.fastq.gz | RNA-Seq | 432.5 MB |
| Hugo-E2_S79_L002_R1_001.fastq.gz | RNA-Seq | 623.7 MB |
| Hugo-E3_S80_L002_R1_001.fastq.gz | RNA-Seq | 571.2 MB |
| Hugo-E4_S32_L002_R1_001.fastq.gz | RNA-Seq | 550.4 MB |
| Hugo-E5_S81_L002_R1_001.fastq.gz | RNA-Seq | 480.7 MB |
| Hugo-E6_S82_L002_R1_001.fastq.gz | RNA-Seq | 515.3 MB |
| Hugo-E7_S33_L002_R1_001.fastq.gz | RNA-Seq | 456.3 MB |
| Hugo-E8_S83_L002_R1_001.fastq.gz | RNA-Seq | 474.5 MB |
| Hugo-F1_S84_L002_R1_001.fastq.gz | RNA-Seq | 504.2 MB |
| Hugo-F2_S34_L002_R1_001.fastq.gz | RNA-Seq | 498.8 MB |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| HM-OT-10_S10_L001_R1_001.fastq.gz | RNA-Seq | 813.2 MB |
| HM-OT-11_S11_L001_R1_001.fastq.gz | RNA-Seq | 508.4 MB |
| HM-OT-12_S12_L001_R1_001.fastq.gz | RNA-Seq | 563.3 MB |
| HM-OT-13_S13_L001_R1_001.fastq.gz | RNA-Seq | 724.0 MB |
| HM-OT-14_S14_L001_R1_001.fastq.gz | RNA-Seq | 568.2 MB |
| HM-OT-5_S5_L001_R1_001.fastq.gz | RNA-Seq | 663.2 MB |
| HM-OT-6_S6_L001_R1_001.fastq.gz | RNA-Seq | 681.5 MB |
| HM-OT-7_S7_L001_R1_001.fastq.gz | RNA-Seq | 632.3 MB |
| HM-OT-8_S8_L001_R1_001.fastq.gz | RNA-Seq | 544.0 MB |
| HM-OT-9_S9_L001_R1_001.fastq.gz | RNA-Seq | 715.2 MB |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| D10_S18_L001_R1_001.fastq.gz | RNA-Seq | 273.6 MB |
| D11_S19_L001_R1_001.fastq.gz | RNA-Seq | 124.6 MB |
| D12_S20_L001_R1_001.fastq.gz | RNA-Seq | 406.1 MB |
| D2_S12_L001_R1_001.fastq.gz | RNA-Seq | 270.0 MB |
| D3_S13_L001_R1_001.fastq.gz | RNA-Seq | 243.5 MB |
| D4_S14_L001_R1_001.fastq.gz | RNA-Seq | 314.6 MB |
| D5_S15_L001_R1_001.fastq.gz | RNA-Seq | 269.5 MB |
| D8_S16_L001_R1_001.fastq.gz | RNA-Seq | 280.6 MB |
| D9_S17_L001_R1_001.fastq.gz | RNA-Seq | 235.0 MB |
| H1_S21_L001_R1_001.fastq.gz | RNA-Seq | 300.6 MB |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (4)
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| Torin_RS_01_S1_L004_R1_001.fastq.gz | RNA-Seq | 2.0 GB |
| Torin_RS_02_S2_L004_R1_001.fastq.gz | RNA-Seq | 4.8 GB |
| Torin_RS_03_S3_L004_R1_001.fastq.gz | RNA-Seq | 3.4 GB |
| Torin_RS_04_S4_L004_R1_001.fastq.gz | RNA-Seq | 4.2 GB |
| Torin_RS_05_S5_L004_R1_001.fastq.gz | RNA-Seq | 3.9 GB |
| Torin_RS_06_S6_L004_R1_001.fastq.gz | RNA-Seq | 2.9 GB |
| Torin_RS_09_S9_L004_R1_001.fastq.gz | RNA-Seq | 2.9 GB |
| Torin_RS_10_S10_L004_R1_001.fastq.gz | RNA-Seq | 4.2 GB |
| Torin_RS_11_S11_L004_R1_001.fastq.gz | RNA-Seq | 3.1 GB |
| Torin_RS_12_S12_L004_R1_001.fastq.gz | RNA-Seq | 4.5 GB |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| 15_S15_L001_R1_001.fastq.gz | RNA-Seq | 12.8 MB |
| 16_S16_L001_R1_001.fastq.gz | RNA-Seq | 13.9 MB |
| 17_S17_L001_R1_001.fastq.gz | RNA-Seq | 12.4 MB |
| 18_S18_L001_R1_001.fastq.gz | RNA-Seq | 9.8 MB |
| 19_S19_L001_R1_001.fastq.gz | RNA-Seq | 14.2 MB |
| 20_S20_L001_R1_001.fastq.gz | RNA-Seq | 14.9 MB |
| 21_S21_L001_R1_001.fastq.gz | RNA-Seq | 8.8 MB |
| 22_S22_L001_R1_001.fastq.gz | RNA-Seq | 7.9 MB |
| 23_S23_L001_R1_001.fastq.gz | RNA-Seq | 11.1 MB |
| 24_S24_L001_R1_001.fastq.gz | RNA-Seq | 9.7 MB |
Potentially related datasets 6
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.
| Accession | Source | Title |
|---|---|---|
| GSE77634 | GSE · GEO GEO ↗ | Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites |
| GSE155729 | GSE · GEO GEO ↗ | Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes |
| GSE91895 | GSE · GEO GEO ↗ | eCLIP from K562 (ENCSR584TCR) |
| GSE263371 | GSE · GEO GEO ↗ | An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP] |
| GSE240521 | GSE · GEO GEO ↗ | An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ] |
| GSE240014 | GSE · GEO GEO ↗ | An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP] |
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| [TEST] Example eCLIP processing pipeline kb-test-seed | eCLIP | 3 |
Funding 8 grants
| Grant | Funder |
|---|---|
| S10 OD026929 | NIH HHS (United States) |
| R01 HG004659 | NHGRI NIH HHS (United States) |
| U24 HG011735 | NHGRI NIH HHS (United States) |
| RF1 MH126719 | NIMH NIH HHS (United States) |
| R01 HG011864 | NHGRI NIH HHS (United States) |
| R35 GM144121 | NIGMS NIH HHS (United States) |
| P30 CA014195 | NCI NIH HHS (United States) |
| S10 OD025052 | NIH HHS (United States) |