A quantitative map of human primary microRNA processing sites

Kim, Ki Jun; Baek, Sungmin; Lee, Young-Yoon; Bastiaanssen, Carolien; Kim, Jeesoo; Kim, Hae-Dong; Kim, V. Narry

doi:10.1016/j.molcel.2021.07.002

Cited by 66 publications

(103 citation statements)

References 118 publications

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“… Note: For optimal aeration during suspension culture, we keep the media volume below 20% of that of the culture bottle. After cell doubling (i.e., 6.0E5 cells/mL), add the plasmids (pX-DROSHA-FLAG and pX-DGCR8-HA constructs) ( Kim et al., 2021 ) to the final concentration of 0.15 μg/mL each (together 0.3 μg/mL DNA) directly to the suspension culture and then shake the culture bottle briefly. Add linear polyethylenimine (PEI) to the suspension culture (final 3 μg/mL) and then shake the culture bottle briefly.…”

Section: Step-by-step Methods Detailsmentioning

confidence: 99%

“…After cell doubling (i.e., 6.0E5 cells/mL), add the plasmids (pX-DROSHA-FLAG and pX-DGCR8-HA constructs) ( Kim et al., 2021 ) to the final concentration of 0.15 μg/mL each (together 0.3 μg/mL DNA) directly to the suspension culture and then shake the culture bottle briefly.…”

Section: Step-by-step Methods Detailsmentioning

confidence: 99%

“…The sequencing data generated by using this protocol are available at GEO under accession number GSE174223 ( Kim et al., 2021 ).…”

Section: Data and Code Availabilitymentioning

confidence: 99%

“…Moreover, cis -acting elements can be examined by replacing the wild-type pri-miRNAs with mutant variants. For complete details on the use and execution of this profile, please refer to Kim et al. (2021) .…”

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confidence: 99%

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High-throughput in vitro processing of human primary microRNA by the recombinant microprocessor

Kim

2022

STAR Protocols

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Summary We describe a protocol to conduct a high-throughput in vitro processing assay, using 1,881 human primary microRNAs (pri-miRNAs) and recombinant Microprocessor complex, followed by deep sequencing library generation. This comprehensive approach allows the mapping of cleavage sites and the measurement of processing efficiency of a large number of substrates simultaneously. Our protocol is readily modifiable to investigate the effects of chemicals and regulatory proteins. Moreover, cis -acting elements can be examined by replacing the wild-type pri-miRNAs with mutant variants. For complete details on the use and execution of this profile, please refer to Kim et al. (2021) .

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Section: Step-by-step Methods Detailsmentioning

confidence: 99%

Section: Step-by-step Methods Detailsmentioning

confidence: 99%

“…The sequencing data generated by using this protocol are available at GEO under accession number GSE174223 ( Kim et al., 2021 ).…”

Section: Data and Code Availabilitymentioning

confidence: 99%

mentioning

confidence: 99%

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High-throughput in vitro processing of human primary microRNA by the recombinant microprocessor

Kim

2022

STAR Protocols

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“…MiRNA is a type of endogenous ncRNA with regulatory functions ( 76 ). It is processed by nucleases from longer primary transcripts and is 20-25 nucleotides long.…”

Section: Ectopic Expression Of Mirnas Promotes Chemotherapeutic Resistance In Ovarian Cancermentioning

confidence: 99%

The Non-Coding RNAs Inducing Drug Resistance in Ovarian Cancer: A New Perspective for Understanding Drug Resistance

Gong

Cao

et al. 2021

Front. Oncol.

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Ovarian cancer, a common malignant tumor, is one of the primary causes of cancer-related deaths in women. Systemic chemotherapy with platinum-based compounds or taxanes is the first-line treatment for ovarian cancer. However, resistance to these chemotherapeutic drugs worsens the prognosis. The underlying mechanism of chemotherapeutic resistance in ovarian cancer remains unclear. Non-coding RNAs, including long non-coding RNAs, microRNAs, and circular RNAs, have been implicated in the development of drug resistance. Abnormally expressed non-coding RNAs can promote ovarian cancer resistance by inducing apoptosis inhibition, protective autophagy, abnormal tumor cell proliferation, epithelial-mesenchymal transition, abnormal glycolysis, drug efflux, and cancer cell stemness. This review summarizes the role of non-coding RNAs in the development of chemotherapeutic resistance in ovarian cancer, including their mechanisms, targets, and potential signaling pathways. This will facilitate the development of novel chemotherapeutic agents that can target these non-coding RNAs and improve ovarian cancer treatment.

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Sensing miRNAs for Disease Diagnostics

et al. 2022

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AbstractmiRNAs are short nucleic acid sequences that regulate gene expression and are important biomarkers for disease diagnostics. In this Review, we overview the biogenesis and functions of miRNAs. The recent progress of biomarker development based on miRNAs is further discussed. In the end, we summarize the progress on miRNA detection methods towards clinical diagnostics. Although proper tools and standardized methodology in detection are still the bottlenecks for miRNA‐based diagnosis, the challenges are likely to be overcome with the development of new bioanalytical techniques. More importantly, upstream studies to elucidate mechanisms of miRNAs in target recognition and correlation with diseases will further advance the clinical use of miRNAs as biomarkers.

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A quantitative map of human primary microRNA processing sites

Cited by 66 publications

References 118 publications

High-throughput in vitro processing of human primary microRNA by the recombinant microprocessor

High-throughput in vitro processing of human primary microRNA by the recombinant microprocessor

The Non-Coding RNAs Inducing Drug Resistance in Ovarian Cancer: A New Perspective for Understanding Drug Resistance

Sensing miRNAs for Disease Diagnostics

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