Non-microRNA binding competitively inhibits LIN28 regulation.
Frederick E Tan, Shashank Sathe, Emily C Wheeler, Gene W Yeo
Cell reports · 2021 · Vol. 36 (6) · pp. 109517
Abstract
RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct regulation of let-7 miRNA biogenesis, is also indirectly regulated by its widespread binding of non-miRNA transcripts. Approximately 99% of LIN28 binding sites are found on non-miRNA transcripts, like protein coding and ribosomal RNAs. These sites are bound specifically and strongly, but they do not appear to mediate direct post-transcriptional regulation. Instead, non-miRNA sites act to sequester LIN28 protein and effectively change its functional availability, thus impeding the regulation of let-7 in cells. Together, these data show that the binding properties of the transcriptome broadly influence the ability of an RBP to mediate changes in RNA metabolism and gene expression.
Linked datasets 2
A transcriptome-wide divergence in protein translation scales with LIN28B expression
Mus musculus
71 data files
| File | Type | Size |
|---|---|---|
| b8p100_smallrnaseq_hek293_ko_l7_ip_S27_L002_R1_001.fastq.gz | RIP-Seq | 335.9 MB |
| b8p100_smallrnaseq_hek293_ko_l7_total_S23_L002_R1_001.fastq… | ncRNA-Seq | 457.6 MB |
| b8p100_smallrnaseq_hek293_ko_wt_ip_S25_L002_R1_001.fastq.gz | RIP-Seq | 304.6 MB |
| b8p100_smallrnaseq_hek293_ko_wt_total_S21_L002_R1_001.fastq… | ncRNA-Seq | 563.8 MB |
| b8p100_smallrnaseq_hek293_x3_l7_ip_S28_L002_R1_001.fastq.gz | RIP-Seq | 241.0 MB |
| b8p100_smallrnaseq_hek293_x3_l7_total_S24_L002_R1_001.fastq… | ncRNA-Seq | 509.1 MB |
| b8p100_smallrnaseq_hek293_x3_wt_ip_S26_L002_R1_001.fastq.gz | RIP-Seq | 341.6 MB |
| b8p100_smallrnaseq_hek293_x3_wt_total_S22_L002_R1_001.fastq… | ncRNA-Seq | 617.8 MB |
| b8p37_a9_input_let7_S1_L003_R1_001.fastq.gz | RNA-Seq | 857.6 MB |
| b8p37_a9_input_S11_L004_R1_001.fastq.gz | RNA-Seq | 912.5 MB |
| b8p37_a9_polysome_let7_S6_L003_R1_001.fastq.gz | OTHER | 274.7 MB |
| b8p37_a9_polysome_S16_L004_R1_001.fastq.gz | OTHER | 279.9 MB |
| b8p37_x1_input_S12_L004_R1_001.fastq.gz | RNA-Seq | 862.4 MB |
| b8p37_x1_polysome_S17_L004_R1_001.fastq.gz | OTHER | 284.3 MB |
| b8p37_x2_input_S13_L004_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| b8p37_x2_polysome_S18_L004_R1_001.fastq.gz | OTHER | 214.5 MB |
| b8p37_x3_input_S14_L004_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| b8p37_x3_polysome_S19_L004_R1_001.fastq.gz | OTHER | 344.3 MB |
| b8p37_x4_input_S15_L004_R1_001.fastq.gz | RNA-Seq | 987.2 MB |
| b8p37_x4_polysome_S20_L004_R1_001.fastq.gz | OTHER | 255.7 MB |
| PX0_S52_L006_R1_001.fastq.gz | OTHER | 1.8 GB |
| PX1_S53_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| PX2_S54_L006_R1_001.fastq.gz | OTHER | 1.7 GB |
| PX3_S55_L006_R1_001.fastq.gz | OTHER | 1.7 GB |
| PX4_S56_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| PX4_S56_L006_R2_001.fastq.gz | OTHER | 1.5 GB |
| SRR6497056_GSM2942714 | OTHER | 279.0 MB |
| SRR6497057_GSM2942715 | OTHER | 284.0 MB |
| SRR6497058 | OTHER | 214.5 MB |
| SRR6497058_GSM2942716 | OTHER | 214.0 MB |
| SRR6497059 | OTHER | 344.3 MB |
| SRR6497059_GSM2942717 | OTHER | 344.0 MB |
| SRR6497060 | OTHER | 255.7 MB |
| SRR6497060_GSM2942718 | OTHER | 255.0 MB |
| SRR6497061_GSM2942719 | RNA-Seq | 912.0 MB |
| SRR6497062_GSM2942720 | RNA-Seq | 862.0 MB |
| SRR6497063_GSM2942721 | RNA-Seq | 1.2 GB |
| SRR6497064_GSM2942722 | RNA-Seq | 1.2 GB |
| SRR6497065_GSM2942723 | RNA-Seq | 987.0 MB |
| SRR6497066_GSM2942724 | OTHER | 1.8 GB |
| SRR6497067_GSM2942725 | OTHER | 1.5 GB |
| SRR6497068_GSM2942726 | OTHER | 1.7 GB |
| SRR6497069_GSM2942727 | OTHER | 1.7 GB |
| SRR6497070_GSM2942728 | OTHER | 1.5 GB |
| SRR6497071 | RNA-Seq | 2.0 GB |
| SRR6497071_GSM2942729 | RNA-Seq | 2.0 GB |
| SRR6497072_GSM2942730 | RNA-Seq | 1.4 GB |
| SRR6497073_GSM2942731 | RNA-Seq | 1.3 GB |
| SRR6497074 | RNA-Seq | 1.6 GB |
| SRR6497074_GSM2942732 | RNA-Seq | 1.6 GB |
| SRR6497075 | RNA-Seq | 1.8 GB |
| SRR6497075_GSM2942733 | RNA-Seq | 1.8 GB |
| SRR6497076_GSM2942734 | RIP-Seq | 335.0 MB |
| SRR6497077_GSM2942735 | ncRNA-Seq | 457.0 MB |
| SRR6497078_GSM2942736 | RIP-Seq | 304.0 MB |
| SRR6497079 | ncRNA-Seq | 563.8 MB |
| SRR6497079_GSM2942737 | ncRNA-Seq | 563.0 MB |
| SRR6497080_GSM2942738 | RIP-Seq | 241.0 MB |
| SRR6497081 | ncRNA-Seq | 509.1 MB |
| SRR6497081_GSM2942739 | ncRNA-Seq | 509.0 MB |
| SRR6497082_GSM2942740 | RIP-Seq | 341.0 MB |
| SRR6497083 | ncRNA-Seq | 617.8 MB |
| SRR6497083_GSM2942741 | ncRNA-Seq | 617.0 MB |
| SRR6497084_GSM2942742 | OTHER | 274.0 MB |
| SRR6497085 | RNA-Seq | 857.6 MB |
| SRR6497085_GSM2942743 | RNA-Seq | 857.0 MB |
| TX0_S47_L006_R1_001.fastq.gz | RNA-Seq | 2.0 GB |
| TX1_S48_L006_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| TX2_S49_L006_R1_001.fastq.gz | RNA-Seq | 1.3 GB |
| TX3_S50_L006_R1_001.fastq.gz | RNA-Seq | 1.6 GB |
| TX4_S51_L006_R1_001.fastq.gz | RNA-Seq | 1.8 GB |
Non-microRNA Binding Competitively Inhibits LIN28 Regulation
Mus musculus
76 data files
| File | Type | Size |
|---|---|---|
| dd-Cit-P-1_S5_L007_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| dd-Cit-P-2_S6_L007_R1_001.fastq.gz | RNA-Seq | 1.3 GB |
| dd-Cit-T-1_S1_L007_R1_001.fastq.gz | RNA-Seq | 1.1 GB |
| dd-Cit-T-2_S2_L007_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| dd-HpK-P-1_S7_L007_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| dd-HpK-P-2_S8_L007_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| dd-HpK-T-1_S3_L007_R1_001.fastq.gz | RNA-Seq | 1.5 GB |
| dd-HpK-T-2_S4_L007_R1_001.fastq.gz | RNA-Seq | 1.6 GB |
| HPK_mESCs_IN7_mock_R1_merged.fastq.gz | RNA-Seq | 1.2 GB |
| HPK_mESCs_IP3_mock_S20_L007_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| HPK_mESCs_IP7_mock_R1_merged.fastq.gz | RNA-Seq | 1.2 GB |
| Hpk_mock_1_poly_S7_L001_R1_001.fastq.gz | RNA-Seq | 793.0 MB |
| Hpk_mock_1_S5_L001_R1_001.fastq.gz | RNA-Seq | 927.7 MB |
| Hpk_mock_2_poly_S19_L002_R1_001.fastq.gz | RNA-Seq | 842.0 MB |
| Hpk_mock_2_S17_L002_R1_001.fastq.gz | RNA-Seq | 874.2 MB |
| LIN28B_PHI_1_CLIP_R1_S32_L002_R1_A01_B06.fastq.gz | RNA-Seq | 460.8 MB |
| LIN28B_PHI_1_CLIP_R2_S24_L002_R1_A01_B06.fastq.gz | RNA-Seq | 305.6 MB |
| LIN28B_PHI_1_INPUT_R1_S29_L002_R1.fastq.gz | RNA-Seq | 1.2 GB |
| LIN28B_PHI_1_INPUT_R2_S21_L002_R1.fastq.gz | RNA-Seq | 786.1 MB |
| LIN28B_PHI_2_CLIP_R1_S31_L002_R1_C01_D08.fastq.gz | RNA-Seq | 420.8 MB |
| LIN28B_PHI_2_CLIP_R2_S23_L002_R1_C01_D08.fastq.gz | RNA-Seq | 361.7 MB |
| LIN28B_PHI_2_INPUT_R1_S30_L002_R1.fastq.gz | RNA-Seq | 1.1 GB |
| LIN28B_PHI_2_INPUT_R2_S22_L002_R1.fastq.gz | RNA-Seq | 1009.7 MB |
| LIN28B_PHI_3_CLIP_R1_S28_L002_R1_A04_F05.fastq.gz | RNA-Seq | 439.3 MB |
| LIN28B_PHI_3_CLIP_R2_S20_L002_R1_A04_F05.fastq.gz | RNA-Seq | 425.0 MB |
| LIN28B_PHI_3_INPUT_R1_S25_L002_R1.fastq.gz | RNA-Seq | 715.9 MB |
| LIN28B_PHI_3_INPUT_R2_S17_L002_R1.fastq.gz | RNA-Seq | 1.0 GB |
| LIN28B_PHI_4_CLIP_R1_S27_L002_R1_X2A_X2B.fastq.gz | RNA-Seq | 445.6 MB |
| LIN28B_PHI_4_CLIP_R2_S19_L002_R1_X2A_X2B.fastq.gz | RNA-Seq | 783.6 MB |
| LIN28B_PHI_4_INPUT_R1_S26_L002_R1.fastq.gz | RNA-Seq | 1.1 GB |
| LIN28B_PHI_4_INPUT_R2_S18_L002_R1.fastq.gz | RNA-Seq | 958.2 MB |
| SRR14820418_GSM5385970 | RNA-Seq | 1.2 GB |
| SRR14820419_GSM5385971 | RNA-Seq | 1.3 GB |
| SRR14820420_GSM5385972 | RNA-Seq | 1.1 GB |
| SRR14820421_GSM5385973 | RNA-Seq | 1.4 GB |
| SRR14820422_GSM5385974 | RNA-Seq | 1.2 GB |
| SRR14820423_GSM5385975 | RNA-Seq | 1.2 GB |
| SRR14820424_GSM5385976 | RNA-Seq | 1.5 GB |
| SRR14820425_GSM5385977 | RNA-Seq | 1.6 GB |
| SRR14820426_GSM5385978 | RNA-Seq | 927.0 MB |
| SRR14820427_GSM5385979 | RNA-Seq | 793.0 MB |
| SRR14820428_GSM5385980 | RNA-Seq | 874.0 MB |
| SRR14820429_GSM5385981 | RNA-Seq | 841.0 MB |
| SRR14820430_GSM5385982 | RNA-Seq | 860.0 MB |
| SRR14820431_GSM5385983 | RNA-Seq | 785.0 MB |
| SRR14820432_GSM5385984 | RNA-Seq | 874.0 MB |
| SRR14820433_GSM5385985 | RNA-Seq | 910.0 MB |
| SRR14820434_GSM5385986 | RNA-Seq | 1.2 GB |
| SRR14820435_GSM5385987 | RNA-Seq | 1.4 GB |
| SRR14820436_GSM5385988 | RNA-Seq | 1.2 GB |
| SRR14820437_GSM5385989 | RNA-Seq | 1.1 GB |
| SRR14820438_GSM5385990 | RNA-Seq | 1.1 GB |
| SRR14820439_GSM5385991 | RNA-Seq | 1.4 GB |
| SRR14820440_GSM5385992 | RNA-Seq | 460.0 MB |
| SRR14820441_GSM5385993 | RNA-Seq | 305.0 MB |
| SRR14820442_GSM5385994 | RNA-Seq | 420.0 MB |
| SRR14820443_GSM5385995 | RNA-Seq | 361.0 MB |
| SRR14820444_GSM5385996 | RNA-Seq | 439.0 MB |
| SRR14820445_GSM5385997 | RNA-Seq | 424.0 MB |
| SRR14820446_GSM5385998 | RNA-Seq | 445.0 MB |
| SRR14820447_GSM5385999 | RNA-Seq | 783.0 MB |
| SRR14820448_GSM5386000 | RNA-Seq | 1.2 GB |
| SRR14820449_GSM5386001 | RNA-Seq | 786.0 MB |
| SRR14820450_GSM5386002 | RNA-Seq | 1.1 GB |
| SRR14820451_GSM5386003 | RNA-Seq | 1009.0 MB |
| SRR14820452_GSM5386004 | RNA-Seq | 715.0 MB |
| SRR14820453_GSM5386005 | RNA-Seq | 1.0 GB |
| SRR14820454_GSM5386006 | RNA-Seq | 1.1 GB |
| SRR14820455_GSM5386007 | RNA-Seq | 958.0 MB |
| V6_5_mESCs_IN1_mock_R1_merged.fastq.gz | RNA-Seq | 1.1 GB |
| V6_5_mESCs_IP1_mock_S19_L007_R1_001.fastq.gz | RNA-Seq | 1.1 GB |
| V6_5_mESCs_IP5_mock_S21_L007_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| V6_5_mock_1_poly_S3_L001_R1_001.fastq.gz | RNA-Seq | 785.1 MB |
| V6_5_mock_1_S1_L001_R1_001.fastq.gz | RNA-Seq | 860.6 MB |
| V6_5_mock_2_poly_S15_L002_R1_001.fastq.gz | RNA-Seq | 910.9 MB |
| V6_5_mock_2_S13_L002_R1_001.fastq.gz | RNA-Seq | 874.1 MB |
Potentially related datasets 2
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 |
|---|---|---|---|
| GSE178259 eCLIP Data Processing geo_data_processing | eCLIP | 6 | GSE178259 |
Funding 3 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| T32 GM008666 | NIGMS NIH HHS (United States) |
| U54 HG007005 | NHGRI NIH HHS (United States) |