Predicting Drosha and Dicer Cleavage Sites with DeepMirCut

Bell, Jimmy D.; Hendrix, David A.

doi:10.3389/fmolb.2021.799056

Cited by 3 publications

(4 citation statements)

References 51 publications

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“…For twelve members, the conserved seed sequence is nested in the 5p-miRNA, whereas for m202, a more distant family member, the conserved seed sequence is in the 3p-miRNA [9]. Dicer cleavage sites are fairly conserved for the 5p let-7, with a UU^(G/U)N consensus at the 5p site and a (C/A)A^CU at the 3p site, fitting previous observations for a strong preference for a uracil nucleotide upstream to the 5p cleavage site and a cytosine nucleotide downstream to the 3p site [37,58]. For the 3p let-7 (miR-202), the cleavage sites are different: 5p (UG^AG) and 3p (AA^AG).…”

Section: Secondary Structure Determination Of the Let-7 Pre-mirnassupporting

confidence: 81%

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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Section: Secondary Structure Determination Of the Let-7 Pre-mirnassupporting

confidence: 81%

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

Dadhwal

Samy

Bouvette

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“… 28 https://bedtools.readthedocs.io/en/latest/ DeepMirCut Bell et al. 29 https://github.com/JimBell/deepMirCut miRanda Enright et al. 30 https://cbio.mskcc.org/miRNA2003/miranda.html FASTX-Toolkit Hannon et al.…”

Section: Methodsmentioning

confidence: 99%

“…A neural network-based algorithm DeepMirCut 29 was applied to predict cleavage sites for Drosha and Dicer on the 165 hairpin structures (30 nt extended on each end) using sequence, dot-bracket structure array, and RNA secondary structures context, thereby confirming the region of the precursor resulting in a potential mature miRNA.…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection

Tucker,

Wong,

Marri

et al. 2024

iScience

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“…In order to evaluate the contribution of editing the hsa-mir21 and hsa-mir-29c loci to the formation of the corresponding pri-miRNA duplexes, we performed in silico folding using the "MFold" web server [64]. With the help of the deepMirCut software package [65], we identified the putative processing sites for Droshaand Dicer-RNAses for the resulting duplexes, and a number of mature 5p-and 3p-miRNAs were predicted.…”

Section: Analysis Of the Genome Editing Efficiencymentioning

confidence: 99%

Advances and Obstacles in Using CRISPR/Cas9 Technology for Non-Coding RNA Gene Knockout in Human Mesenchymal Stromal Cells

Basalova,

Illarionova,

Skryabina

et al. 2023

ncRNA

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Non-coding RNA (ncRNAs) genes have attracted increasing attention in recent years due to their widespread involvement in physiological and pathological processes and regulatory networks. The study of the function and molecular partners of ncRNAs opens up opportunities for the early diagnosis and treatment of previously incurable diseases. However, the classical “loss-of-function” approach in ncRNA function analysis is challenged due to some specific issues. Here, we have studied the potency of two CRISPR/Cas9 variants, wild-type (SpCas9wt) and nickase (SpCas9D10A) programmable nucleases, for the editing of extended DNA sequences in human mesenchymal stromal cells (MSCs). Editing the genes of fibrosis-related hsa-miR-21-5p and hsa-miR-29c-3p, we have shown that a pair of SpCas9D10A molecules can effectively disrupt miRNA genes within the genomes of MSCs. This leads not only to a decrease in the level of knockout miRNA in MSCs and MSC-produced extracellular vesicles, but also to a change in cell physiology and the antifibrotic properties of the cell secretome. These changes correlate well with previously published data for the knockdown of certain miRNAs. The proposed approach can be used to knock out ncRNA genes within the genomes of MSCs or similar cell types in order to study their function in biological processes.

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Predicting Drosha and Dicer Cleavage Sites with DeepMirCut

Cited by 3 publications

References 51 publications

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

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

SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection

Advances and Obstacles in Using CRISPR/Cas9 Technology for Non-Coding RNA Gene Knockout in Human Mesenchymal Stromal Cells

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