Dicer‐Processed Small RNAs: Rules and Exceptions

Langenberger, David; Çakır, Mehmet Volkan; Hoffmann, Steve; Stadler, Peter F.

doi:10.1002/jez.b.22481

Cited by 57 publications

(47 citation statements)

References 67 publications

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“…Especially efficient was Dicer-1 depletion for candidate discrimination, as this approach allowed discarding 2,117 out of the 2,675 candidates in a first filter, results that are in concordance with those of other authors252627. It is worth noting, however, that Dicer-1 depletion did not significantly affect 10% of the conserved miRNA, which might be Dicer-1 independent miRNAs28.…”

Section: Discussionsupporting

confidence: 78%

The microRNA toolkit of insects

Ylla

Fromm

Piulachs

et al. 2016

Sci Rep

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Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.

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Section: Discussionsupporting

confidence: 78%

The microRNA toolkit of insects

Ylla

Fromm

Piulachs

et al. 2016

Sci Rep

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“…Different classes of probes can receive different weights depending on their reliability as invariant controls. Affymetrix miRNA microarrays contain about one-fifth of non-miRNA small RNA probes (small nucleolar RNAssnoRNAs-comprising small Cajal body-specific RNAs, and C/D box and H/ACA box small RNAs), which are mostly independent of the miRNA processing pathway (Langenberger et al 2013). We postulated that such non-miRNA probes from the Affymetrix platform could be used as invariant probes for cyclic loess.…”

Section: Normexp Background Correction With Cyclic Loess Normalizationmentioning

confidence: 99%

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

Tong

et al. 2013

RNA

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Recent studies have established that mutations or deletions in microRNA (miRNA) processing enzymes resulting in a global decrease of miRNA expression are frequent across cancers and can be associated with a poorer prognosis. While very popular in miRNA profiling studies, it remains unclear whether miRNA microarrays are suited or not to accurately detecting global miRNA decreases seen in cancers. In this work, we analyzed the miRNA profiles of samples with global miRNA decreases using Affymetrix miRNA microarrays following the inducible genetic deletion of Dicer1. Surprisingly, up to a third of deregulated miRNAs identified upon Dicer1 depletion were found to be up-regulated following standard robust multichip average (RMA) background correction and quantile normalization, indicative of normalization bias. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs. These findings were validated in samples from patients with prostate cancer, where conjugation of robust normal-exponential background correction with cyclic loess normalization and array weights correctly identified the greatest number of decreased miRNAs, and the lowest amount of false-positive up-regulated miRNAs. These findings highlight the importance of miRNA microarray normalization for the detection of miRNAs that are truly differentially expressed and suggest that the use of cyclic loess based on non-miRNA small RNAs can help to improve the sensitivity and specificity of miRNA profiling in cancer samples with global miRNA decrease.

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“…5 F ). Conversely, others and we have shown that there is at least 2-fold decrease of miR-21 in the Dicer −/− HCT116 cells [34], [44]. The data indicate that the expression of the SNORD44 sdRNAs is independent of the canonical miRNA-processing pathway.…”

Section: Resultsmentioning

confidence: 47%

“…Dicer has been implicated in the processing of H/ACA snoRNA [30] but not box C/D snoRNAs [44]. We hence explored the possibility that the miRNA pathway is involved in the processing of the SNORD44-derived fragments.…”

Section: Resultsmentioning

confidence: 99%

RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

et al. 2014

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Small non-coding RNAs represent RNA species that are not translated to proteins, but which have diverse and broad functional activities in physiological and pathophysiological states. The knowledge of these small RNAs is rapidly expanding in part through the use of massive parallel (deep) sequencing efforts. We present here the first deep sequencing of small RNomes in subcellular compartments with particular emphasis on small RNAs (sRNA) associated with the nucleolus. The vast majority of the cellular, cytoplasmic and nuclear sRNAs were identified as miRNAs. In contrast, the nucleolar sRNAs had a unique size distribution consisting of 19–20 and 25 nt RNAs, which were predominantly composed of small snoRNA-derived box C/D RNAs (termed as sdRNA). Sequences from 47 sdRNAs were identified, which mapped to both 5′ and 3′ ends of the snoRNAs, and retained conserved box C or D motifs. SdRNA reads mapping to SNORD44 comprised 74% of all nucleolar sdRNAs, and were confirmed by Northern blotting as comprising both 20 and 25 nt RNAs. A novel 120 nt SNORD44 form was also identified. The expression of the SNORD44 sdRNA and 120 nt form was independent of Dicer/Drosha–mediated processing pathways but was dependent on the box C/D snoRNP proteins/sno-ribonucleoproteins fibrillarin and NOP58. The 120 nt SNORD44-derived RNA bound to fibrillarin suggesting that C/D sno-ribonucleoproteins are involved in regulating the stability or processing of SNORD44. This study reveals sRNA cell-compartment specific expression and the distinctive unique composition of the nucleolar sRNAs.

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Dicer‐Processed Small RNAs: Rules and Exceptions

Cited by 57 publications

References 67 publications

The microRNA toolkit of insects

The microRNA toolkit of insects

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

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