Structure of the human DICER–pre-miRNA complex in a dicing state

Lee, Young-Yoon; Lee, Hansol; Kim, Haedong; Kim, V. Narry; Roh, Sook Young

doi:10.1038/s41586-023-05723-3

Cited by 43 publications

(71 citation statements)

References 64 publications

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“…As described, the Platform-PAZ domain plays an important role in pre-miRNA substrate recognition via binding to the 3′ 2-nt overhang and 5′ phosphate, and docking of these motifs within the domain enables Dicer to produce mature miRNAs of a precise length. , To determine how the disease-relevant Platform-PAZ mutants affect the integrity of small RNA processing, we were eager to probe the ability of the Dicer mutants to produce the expected 5P and 3P cleavage products.…”

Section: Resultsmentioning

confidence: 99%

“…One potential hypothesis is that snord37 uses an alternative counting rule. Typically, counting to determine the precise site at which to cleave mature miRNA products begins at the 3′ or 5′ binding pockets within the Platform-PAZ domain, and cleavage is dependent upon the physical distance between these binding pockets and the RNase III domains. ,− ,, However, more recent studies have revealed a third counting rule, termed the loop counting rule, which uses the single-stranded regions of the RNA substrate, either an internal bulge or a terminal loop, to anchor the cleavage site 2 nt upstream of this structural motif. , Thus, it is possible that loop interactions drive the binding and processing of snord37, and future studies should be directed at investigating this question as well as global analysis of small RNA processing affected by these Dicer mutants in cellular disease models.…”

Section: Resultsmentioning

confidence: 99%

“…Nonetheless, our work contributes new knowledge to how Dicer activity can be altered by changes in one of its noncatalytic domains and adds to recent findings characterizing the significance of cancerassociated mutations in Dicer's Platform-PAZ domain. 28 ■ ASSOCIATED CONTENT * sı Supporting Information…”

Section: ■ Conclusionmentioning

confidence: 99%

“…The Platform-PAZ domain plays an important role in substrate recognition as it contains binding pockets for both the 3′ 2-nt overhang and 5′ phosphate of a pre-miRNA substrate. ,− Disruption of the residues associated with these binding pockets directly affects the binding affinity of Dicer for pre-miRNAs and its ability to produce mature miRNAs of an appropriate length. ,, Interestingly, some Platform-PAZ domain disease mutations are not located within the substrate-binding pockets, and unlike disease mutations found in the RNase III domains, preliminary studies have demonstrated that these mutations impact Dicer’s ability to cleave both 5P and 3P strands. , Thus, we became interested in further examining the functional impact of disease-associated mutations within the Platform-PAZ domain, and herein, we describe our efforts to characterize select mutants using a combination of in vitro biochemical analyses and cellular studies.…”

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confidence: 99%

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Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA

et al. 2023

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Dicer is an RNase III enzyme that is responsible for the maturation of small RNAs such as microRNAs. As Dicer’s cleavage products play key roles in promoting cellular homeostasis through the fine-tuning of gene expression, dysregulation of Dicer activity can lead to several human diseases, including cancers. Mutations in Dicer have been found to induce tumorigenesis and lead to the development of a rare pleiotropic tumor predisposition syndrome found in children and young adults called DICER1 syndrome. These patients harbor germline and somatic mutations in Dicer that lead to defective microRNA processing and activity. While most mutations occur within Dicer’s catalytic RNase III domains, alterations within the Platform-PAZ (Piwi-Argonaute-Zwille) domain also cause loss of microRNA production. Using a combination of in vitro biochemical and cellular studies, we characterized the effect of disease-relevant Platform-PAZ-associated mutations on the processing of a well-studied oncogenic microRNA, pre-microRNA-21. We then compared these results to those of a representative from another Dicer substrate class, the small nucleolar RNA, snord37. From this analysis, we provide evidence that mutations within the Platform-PAZ domain result in differential impacts on RNA binding and processing, adding new insights into the complexities of Dicer processing of small RNA substrates.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: ■ Conclusionmentioning

confidence: 99%

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confidence: 99%

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Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA

et al. 2023

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“…For all pre-let-7 members except 7e, the 5p cleavage site is located exactly at the junction between the paired region and the large loop/bulge region (7a1, 7a2, 7a3, 7d, 7f2, and 7g) or 1-2-nt away (7b, 7c, 7f1, 7i, m98 and m202). For the latter cases, only minor conformational changes, such as base-pair openings or exchanges, would be required to bring the 5p cleavage site in a dicing-compatible conformation, such as the ones seen in recent cryo-EM structures of human Dicer in the dicing state [22,24]. These structural features are consistent with the fact that all prelet-7 substrates are cleaved by Dicer to mainly yield a single 22-nt 5p miRNA product, except for 7e where more than 5% of an additional 23-nt 5p product is observed.…”

Section: Discussionmentioning

confidence: 99%

Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications

Dadhwal

Samy

Bouvette

et al. 2023

Preprint

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The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'mono-uridylation and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rate. Thus, this study extends current knowledge regarding the broad specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.

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Berberine: Potential preventive and therapeutic strategies for human colorectal cancer

Feng,

Lu,

Jiang

et al. 2024

Cell Biochemistry & Function

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Colorectal cancer (CRC) is a common digestive tract tumor, with incidences continuing to rise. Although modern medicine has extended the survival time of CRC patients, its adverse effects and the financial burden cannot be ignored. CRC is a multi‐step process and can be caused by the disturbance of gut microbiome and chronic inflammation's stimulation. Additionally, the presence of precancerous lesions is also a risk factor for CRC. Consequently, scientists are increasingly interested in identifying multi‐target, safe, and economical herbal medicine and natural products. This paper summarizes berberine's (BBR) regulatory mechanisms in the occurrence and development of CRC. The findings indicate that BBR regulates gut microbiome homeostasis and controls mucosal inflammation to prevent CRC. In the CRC stage, BBR inhibits cell proliferation, invasion, and metastasis, blocks the cell cycle, induces cell apoptosis, regulates cell metabolism, inhibits angiogenesis, and enhances chemosensitivity. BBR plays a role in the overall management of CRC. Therefore, using BBR as an adjunct to CRC prevention and treatment could become a future trend in oncology.

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Structure of the human DICER–pre-miRNA complex in a dicing state

Cited by 43 publications

References 64 publications

Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA

Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA

Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications

Berberine: Potential preventive and therapeutic strategies for human colorectal cancer

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