MapToCleave: High-throughput profiling of microRNA biogenesis in living cells

Kang, Wenjing; Fromm, Bastian; Houben, Anna J.S.; Høye, Eirik; Bezdan, Daniela; Arnan, Carme; Thrane, Kim; Asp, Michaela; Johnson, Rory; Biryukova, Inna; Friedländer, Marc R.

doi:10.1016/j.celrep.2021.110015

Cited by 24 publications

(20 citation statements)

References 75 publications

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“…The dsRBD domain of DROSHA recognizes a mismatched GHG motif to place the catalytic center in an appropriate position [22]. This supports the microprocessor cleavage precision [17,22]. In addition, a recent report described that the asymmetric internal loop in the lower stem of pri-miRNAs differentially affects the cleavage of pri-miRNAs on each strand [23].…”

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 57%

“…Therefore, lower basal stem stability is associated with high miRNA expression levels [17,23]. In addition, the profiling of chromatin-associated pri-miRNAs supports the importance of more stable lower basal stems for pri-miRNA processing [17].…”

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 81%

“…The large asymmetric internal loop, that is, large mismatches, inhibits 3p strand cleavage, leading to a single cleavage on the 5p strand (5p-nick processing) and decreased miRNA expression [23]. Therefore, lower basal stem stability is associated with high miRNA expression levels [17,23]. In addition, the profiling of chromatin-associated pri-miRNAs supports the importance of more stable lower basal stems for pri-miRNA processing [17].…”

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 97%

“…Efficient pri-miRNA processing requires several pri-miRNA sequence features, including a narrow range of tolerable pri-miRNA stem lengths (35 ± 1 base pairs), a CNNC motif (SRp20/SRSF3-binding motif) 16-18 bp downstream of the DROSHA processing site, a UG motif at the base of the pri-miRNA hairpin, a mismatched GHG motif in the basal stem region, a stable lower basal stem structure (typically less than four mismatches), and a UGU(GUG) motif in the apical loop (Figure 1b) [14][15][16][17]. These features are highly conserved among animals [18].…”

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 99%

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Network Regulation of microRNA Biogenesis and Target Interaction

Komatsu

Kitai

Suzuki

2023

Cells

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MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA–target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA–target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA–target interaction.

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Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 57%

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 81%

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 97%

Section: Structural Basis Of Pri-mirna Processingmentioning

confidence: 99%

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Network Regulation of microRNA Biogenesis and Target Interaction

Komatsu

Kitai

Suzuki

2023

Cells

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“…While CNNC and various other motifs (i.e. UG, mGHG, UGU) are known to be enriched in human pri-miRNAs and conserved in the pri-miRNAs of many organisms from flies to humans, UG, UGU and CNNC are not enriched or conserved in C. elegans pri-miRNAs ( 25 , 26 , 34 ). In contrast, midBMW are found in pri-miRNAs from many organisms, including humans and C. elegans ( 28 , 29 ).…”

Section: Introductionmentioning

confidence: 97%

Dissection of theCaenorhabditis elegans Microprocessor

Nguyễn

Ngo

et al. 2023

Nucleic Acids Research

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Microprocessor (MP) is a complex involved in initiating the biogenesis of microRNAs (miRNAs) by cleaving primary microRNAs (pri-miRNAs). miRNAs are small single-stranded RNAs that play a key role in the post-transcriptional regulation of gene expression. Thus, understanding the molecular mechanism of MP is critical for interpreting the roles of miRNAs in normal cellular processes and during the onset of various diseases. MP comprises a ribonuclease enzyme, DROSHA, and a dimeric RNA-binding protein, which is called DGCR8 in humans and Pasha in Caenorhabditis elegans. DROSHA cleaves stem-loop structures located within pri-miRNAs to generate pre-miRNAs. Although the molecular mechanism of human MP (hMP; hDROSHA-DGCR8) is well understood, that of Caenorhabditis elegans MP (cMP; cDrosha-Pasha) is still largely unknown. Here, we reveal the molecular mechanism of cMP and show that it is distinct from that of hMP. We demonstrate that cDrosha and Pasha measure ∼16 and ∼25 bp along a pri-miRNA stem, respectively, and they work together to determine the site of cMP cleavage in pri-miRNAs. We also demonstrate the molecular basis for their substrate measurement. Thus, our findings reveal a previously unknown molecular mechanism of cMP; demonstrate the differences between the mechanisms of hMP and cMP; and provide a foundation for revealing the mechanisms regulating miRNA expression in different animal species.

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Transcriptome and microRNAome elucidate the mechanism underlying the immunomodulatory effects of dietary CpG oligodeoxynucleotides (CpG ODNs) in Litopenaeus vannamei

Hu,

Chen,

et al. 2024

Aquaculture

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MapToCleave: High-throughput profiling of microRNA biogenesis in living cells

Cited by 24 publications

References 75 publications

Network Regulation of microRNA Biogenesis and Target Interaction

Network Regulation of microRNA Biogenesis and Target Interaction

Dissection of theCaenorhabditis elegans Microprocessor

Transcriptome and microRNAome elucidate the mechanism underlying the immunomodulatory effects of dietary CpG oligodeoxynucleotides (CpG ODNs) in Litopenaeus vannamei

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