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| Status |
Public on Jan 07, 2022 |
| Title |
Non-microRNA Binding Competitively Inhibits LIN28 Regulation |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from LIN28B immunoprecipitation and 2 control input replicates for 4 LIN28B expression conditions in HEK293A (LIN28B_X1, LIN28B_X2, LIN28B_X3, LIN28B_X4). Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from Lin28A immunoprecipitation and 2 control input replicates in mouse ESCs with (HPK_mESCs) and without (V6_5_mESCs) sponge expression. Examination of changes in transcriptome-wide ribosome occupancy in mouse ESCs via total RNA (2 replicates, T) and ribosome-bound RNA (2 replicates, P) for several experimental conditions: (dd-Cit = double Dicer knockout ESCs expressing mock Citrine), (dd-HpK = double Dicer knockout ESCs expressing LIN28 sponge), (V6_5_mock = V6.5 ESCs expressing mock Citrine), (Hpk_mock = V6.5 ESCs expressing LIN28 sponge).
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| Contributor(s) |
Tan FE, Sathe S, Wheeler EC, Yeo GW |
| Citation(s) |
34380031 |
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| Submission date |
Jun 15, 2021 |
| Last update date |
Jan 08, 2022 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
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| Organization name |
UCSD
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| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (38)
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| Relations |
| BioProject |
PRJNA738154 |
| SRA |
SRP324158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE178259_RAW.tar |
254.1 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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