The bulges control in pri-miRNA processing in the position and strand-dependent manner
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ABSTRACT:
PROVIDER: PRJNA663871 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12653304_1.fastq.gz | Fastqsanger.gz | |||
| SRR12653304_2.fastq.gz | Fastqsanger.gz | |||
| SRR12653305_1.fastq.gz | Fastqsanger.gz | |||
| SRR12653305_2.fastq.gz | Fastqsanger.gz | |||
| SRR12653306_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
2021-08-23 | GSE158060 | GEO
Project description:MicroRNAs (miRNAs) play critical roles in gene expression and numerous human diseases. The success of miRNA biogenesis is largely determined by the primary miRNA (pri-miRNA) processing by the DROSHA-DGCR8 complex, called Microprocessor. Here, we analysed the high-throughput pri-miRNA processing assays and secondary structures of pri-miRNAs to investigate the roles of bulges in the pri-miRNA processing. We found that bulges in multiple places control both the cleavage efficiency and accuracy of pri-miRNA processing. These bulges were shown to act on Microprocessor via its catalytic subunit, DROSHA, and function in a position and strand-dependent manner. Interestingly, we discovered that the enriched and conserved bulges, called midB, can correct DROSHA orientation on pri-miRNAs, thereby enhancing production of miRNAs. The revealed functions of the bulges help improve our understanding of pri-miRNA processing and suggest their potential roles in miRNA biogenesis regulation.
| S-EPMC8582997 | biostudies-literature
Project description:Targeted sequencing at Microprocessor cleavage sites in pri-miRNAs to determine processing efficiency of several pri-miRNAs in vivo in one experiment
2020-04-17 | GSE148756 | GEO
Project description:Targeted sequencing at Microprocessor cleavage sites in pri-miRNAs to determine processing efficiency of several pri-miRNAs in vivo in one experiment
2020-05-01 | GSE149631 | GEO
Project description:We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR In the study presented here, a colorrectal cancer cell line (HCT-116) was transiently transfected with Uc.283+A in order to identify putative miRNA targets for Uc.283+A. Variant 1 represents a SNP variant (8x(T) repeat in the sequence). Variant 2 represents a SNP variant (9x(T) repeat in the sequence).
2014-05-01 | E-GEOD-56841 | biostudies-arrayexpress
Project description:We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR
2014-05-01 | GSE56841 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. MicroRNAs are predicted to regulate the expression of more than 60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The dsRNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of pri-miRNAs. Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 25 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to ac quisition of NF90 association, as determined by RNA EMSA. NF90-bound and modulated pri-miRNAs are embedded in introns of host genes and expression of several is concomitantly modulated, including an oncogene implicated in metastasis of hepatocellular carcinoma, TIAM2. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.
2020-05-01 | GSE132341 | GEO
Project description:Human Microprocessor cleaves pri-miRNAs to initiate miRNA biogenesis. The accuracy and efficiency of Microprocessor cleavage ensure appropriate miRNA sequence and expression and thus its proper gene regulation. However, Microprocessor cleaves many pri-miRNAs incorrectly, so it requires assistance from its many cofactors. For example, SRSF3 enhances Microprocessor cleavage by interacting with the CNNC motif in pri-miRNAs. However, whether SRSF3 can function with other motifs and/or requires the motifs in a certain secondary structure is unknown. In addition, the function of SRSF7 (a paralog of SRSF3) in miRNA biogenesis still needs to be discovered. Here, we demonstrated that SRSF7 could stimulate Microprocessor cleavage. In addition, by conducting high-throughput pri-miRNA cleavage assays for Microprocessor and SRSF7 or SRSF3, we demonstrated that SRSF7 and SRSF3 function with the CRC and CNNC motifs, adopting certain secondary structures. In addition, SRSF7 and SRSF3 affect the Microprocessor cleavage sites in human cells. Our findings demonstrate the roles of SRSF7 in miRNA biogenesis and provide a comprehensive view of the molecular mechanism of SRSF7 and SRSF3 in enhancing Microprocessor cleavage.
2023-01-23 | GSE215790 | GEO
Project description:Targeted determination of pri-miRNA processing
| PRJNA625651 | ENA
Project description:Targeted determination of pri-miRNA processing
| PRJNA629495 | ENA