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| Status |
Public on Aug 23, 2021 |
| Title |
The bulges control in pri-miRNA processing in the position and strand-dependent manner |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
The microRNA (miRNA) biogenesis is responsible for the production of miRNAs that play critical roles in gene expression and numerous human diseases. The adequate biogenesis of miRNAs is largely determined by the efficiency and fidelity of primary microRNA (pri-miRNA) processing by Microprocessor. Here, we investigated the roles of a secondary RNA element, an RNA bulge, in pri-miRNA processing. We discovered that the 3p-strand bulges in positions 7-9 from the Microprocessor cleavage sites (midB_7-9) contributes to determining the cleavage sites of Microprocessor, the 5p- and 3p-strand bugles in positions 10-12 (midB_10-12) blocked the unproductive cleavage, and the 3p-strand bulges in positions 6-7 (seedB) inhibited the productive cleavage of Microprocessor. The 5p-strand midB_10-12 was found enriched and conserved in many pri-miRNAs of humans and other organisms. In addition, by analyzing the published Microprocessor-RNA structure and doing mutagenesis, we identified several amino acid residues of Microprocessor that explains a structure basis for the processing inhibition caused by seedB. The revealed functions of bulges in our study improves our understanding of the pri-miRNA processing by Microprocessor and implies their roles in regulating miRNA expression.
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| Overall design |
HCT116 cells were transfected with pcDNA3.0 plasmids encoding pri-mir-342 or its variants. Small RNA sequencing libraries of the transfected cells were generated. The experiment was repeated three times.
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| Contributor(s) |
Nguyen TA, Le TN, Li S, Nguyen TD |
| Citation(s) |
33382955 |
| |
| Submission date |
Sep 16, 2020 |
| Last update date |
Sep 14, 2021 |
| Contact name |
Duc Trung Nguyen |
| E-mail(s) |
[email protected]
|
| Phone |
+582 53345859
|
| Organization name |
The Hong Kong University of Science and Technology
|
| Department |
Life Science
|
| Lab |
Anh Lab
|
| Street address |
Clear Water Bay
|
| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (15)
|
| GSM4787716 |
HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 1 |
| GSM4787717 |
HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 2 |
| GSM4787718 |
HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 3 |
| GSM4787719 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 1 |
| GSM4787720 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 2 |
| GSM4787721 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 3 |
| GSM4787722 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 1 |
| GSM4787723 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 2 |
| GSM4787724 |
HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 3 |
| GSM4787725 |
HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 1 |
| GSM4787726 |
HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 2 |
| GSM4787727 |
HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 3 |
| GSM4787728 |
HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 1 |
| GSM4787729 |
HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 2 |
| GSM4787730 |
HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 3 |
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| Relations |
| BioProject |
PRJNA663871 |
| SRA |
SRP282603 |
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