Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Anne E Conway, Eric L Van Nostrand, Gabriel A Pratt, Stefan Aigner, Melissa L Wilbert, Balaji Sundararaman, Peter Freese, Nicole J Lambert, Shashank Sathe, Tiffany Y Liang, Anthony Essex, Severine Landais, Christopher B Burge, D Leanne Jones, Gene W Yeo
Cell reports · 2016 · Vol. 15 (3) · pp. 666-679
Abstract
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region and binding site levels, IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3' UTR-enriched targets. RNA Bind-N-seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and increase in cell death. For cell adhesion, we find IMP1 maintains levels of integrin mRNA specifically regulating RNA stability of ITGB5 in hPSCs. Additionally, we show that IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles.
Linked datasets 3
Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival
Homo sapiens
Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [RNA-Seq]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| ACMW_12_CTTGTA_L006_R1.fastq.gz | RNA-Seq | 1.3 GB |
| ACMW_4_TGACCA_L006_R1.fastq.gz | RNA-Seq | 1.9 GB |
| ACMW_5_ACAGTG_L006_R1.fastq.gz | RNA-Seq | 893.0 MB |
| ACMW_6_GCCAAT_L006_R1.fastq.gz | RNA-Seq | 1.2 GB |
| ACMW_7_CAGATC_L006_R1.fastq.gz | RNA-Seq | 1.3 GB |
| SRR3187417_GSM2071752 | RNA-Seq | 1.9 GB |
| SRR3187418_GSM2071753 | RNA-Seq | 893.0 MB |
| SRR3187419_GSM2071754 | RNA-Seq | 1.2 GB |
| SRR3187420_GSM2071755 | RNA-Seq | 1.3 GB |
| SRR3187421_GSM2071756 | RNA-Seq | 1.3 GB |
Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [eCLIP-Seq]
Homo sapiens
34 data files
| File | Type | Size |
|---|---|---|
| FOX2-H1ES_S9_R1.A01_RBFOX2_H1ES_1to25_RBFOX2.randomer.fastq… | OTHER | 118.0 MB |
| FOX2-H1ES_S9_R1.B06_RBFOX2_H1ES_1to25_RBFOX2.randomer.fastq… | OTHER | 56.1 MB |
| SF3B4_H1_INPUT_ATTACTCG-CCTATCCT_L005_R1.unassigned.randome… | OTHER | 245.1 MB |
| SRR3187400_GSM2071742 | OTHER | 129.0 MB |
| SRR3187401_GSM2071742 | OTHER | 111.0 MB |
| SRR3187402_GSM2071743 | OTHER | 135.0 MB |
| SRR3187403_GSM2071743 | OTHER | 138.0 MB |
| SRR3187404_GSM2071744 | OTHER | 772.0 MB |
| SRR3187405_GSM2071745 | OTHER | 270.0 MB |
| SRR3187406_GSM2071745 | OTHER | 210.0 MB |
| SRR3187407_GSM2071746 | OTHER | 234.0 MB |
| SRR3187408_GSM2071746 | OTHER | 193.0 MB |
| SRR3187409_GSM2071747 | OTHER | 212.0 MB |
| SRR3187410_GSM2071747 | OTHER | 200.0 MB |
| SRR3187411_GSM2071748 | OTHER | 117.0 MB |
| SRR3187412_GSM2071748 | OTHER | 88.0 MB |
| SRR3187413_GSM2071749 | OTHER | 708.0 MB |
| SRR3187414_GSM2071750 | OTHER | 118.0 MB |
| SRR3187415_GSM2071750 | OTHER | 56.0 MB |
| SRR3187416_GSM2071751 | OTHER | 245.0 MB |
| Stefan-1to25-Imp1_S16_R1.A01_Stefan_1to25_Imp1_IGF2BP1.rand… | OTHER | 129.6 MB |
| Stefan-1to25-Imp1_S16_R1.B06_Stefan_1to25_Imp1_IGF2BP1.rand… | OTHER | 111.4 MB |
| Stefan-1to25-Imp2_S17_R1.C01_Stefan_1to25_Imp2_IGF2BP2.rand… | OTHER | 135.3 MB |
| Stefan-1to25-Imp2_S17_R1.D08fixed_Stefan_1to25_Imp2_IGF2BP2… | OTHER | 138.3 MB |
| Stefan-1to25-Input_S15_R1.unassigned.randomer.fastq.gz | OTHER | 772.3 MB |
| Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.A01_Stefan_IGF2B… | OTHER | 270.4 MB |
| Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.B06_Stefan_IGF2B… | OTHER | 210.2 MB |
| Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.C01_Stefan_IGF2B… | OTHER | 234.8 MB |
| Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.D08fixed_Stefan_… | OTHER | 193.2 MB |
| Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.C01_Stefan_IGF2B… | OTHER | 212.9 MB |
| Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.D08fixed_Stefan_… | OTHER | 200.7 MB |
| Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.A01_Stefan_IgG_04091… | OTHER | 117.9 MB |
| Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.B06_Stefan_IgG_04091… | OTHER | 88.6 MB |
| Stefan_Input_040915_GAGATTCC-ATAGAGGC_R1.unassigned.randome… | OTHER | 708.2 MB |
Potentially related datasets 3
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 |
|---|---|---|
| ENCSR588GYZ | ENCSR · ENCODE | RNA Bind-n-Seq (RBNS) pulldown experiment against IGF2BP2 |
| ENCSR928XOW | ENCSR · ENCODE | RNA Bind-n-Seq (RBNS) pulldown experiment against IGF2BP1/IMP1 |
| GSE78509 | GSE · GEO GEO ↗ | Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival |
Analysis pipelines 3
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE78507 eCLIP Data Processing geo_data_processing | eCLIP | 33 | GSE78507 |
| GSE78508 eCLIP Data Processing geo_data_processing | eCLIP | 5 | GSE78508 |
| GSE78509 eCLIP Data Processing geo_data_processing | eCLIP | 33 | GSE78509 |
Funding 10 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| P30 CA023100 | NCI NIH HHS (United States) |
| T32 GM008666 | NIGMS NIH HHS (United States) |
| T32 GM087237 | NIGMS NIH HHS (United States) |
| U54 HG007005 | NHGRI NIH HHS (United States) |
| U54HG007005 | NHGRI NIH HHS (United States) |
| R01 NS075449 | NINDS NIH HHS (United States) |
| HG004659 | NHGRI NIH HHS (United States) |
| NS075449 | NINDS NIH HHS (United States) |
| HG007005 | NHGRI NIH HHS (United States) |