Sequence Features of Drosha and Dicer Cleavage Sites Affect the Complexity of IsomiRs

Staręga-Rosłan, Julia; Witkos, Tomasz M.; Galka-Marciniak, Paulina; Krzyżosiak, Włodzimierz J.

doi:10.3390/ijms16048110

Cited by 49 publications

(55 citation statements)

References 50 publications

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“…ii) The requirement for the siRNA to contain a 5'-uracil. This appeared to promote more efficient and more precise siRNA biogenesis (Figure 3), which is consistent with studies demonstrating a 5'-U promotes Dicer processing and Argonaute association (27,28). iii) The requirement for nucleotides 21-23 of the siRNA to be perfectly complementary to the target mRNA.…”

Section: Algorithm For Easy and Flexible Design Of Cshrna Templatessupporting

confidence: 86%

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes

Kincaid

Aloisio

Welch

et al. 2017

Preprint

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Section: Algorithm For Easy and Flexible Design Of Cshrna Templatessupporting

confidence: 86%

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes

Kincaid

Aloisio

Welch

et al. 2017

Preprint

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“…We propose that initial endoribonucleolytic cleavages by other enzymes may facilitate Dicer-2 in gaining access to the numerous hot spots, although we cannot rule out the possibility that Dicer-2 may itself be implicated in the initial endoRNase activities. Interestingly, mammalian RNase III class enzymes Dicer and Drosha, both implicated in the microRNA pathway, have been shown to exhibit specific base preferences at the cut site (44), which nevertheless do not match our motif. Further, no eukaryotic RNases with sequence specificity have been identified to date (45), whereas the unique case of RNase Mini-III from Bacillus subtilis that cleaves dsRNA in a sequence-specific manner was discovered recently (46).…”

Section: Discussionmentioning

confidence: 95%

Viral Small-RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection

Zografidis

Nieuwerburgh

Κολλιοπούλου

et al. 2015

J Virol

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The lepidopteran innate immune response against RNA viruses remains poorly understood, while in other insects several studies have highlighted an essential role for the exo-RNAi pathway in combating viral infection. Here, by using deep-sequencing technology for viral small-RNA (vsRNA) assessment, we provide evidence that exo-RNAi is operative in the silkworm Bombyx mori against both persistent and pathogenic infection of B. mori cytoplasmic polyhedrosis virus (BmCPV) which is characterized by a segmented double-stranded RNA (dsRNA) genome. Further, we show that Dicer-2 predominantly targets viral dsRNA and produces 20-nucleotide (nt) vsRNAs, whereas an additional pathway is responsive to viral mRNA derived from segment 10. Importantly, vsRNA distributions, which define specific hot and cold spot profiles for each viral segment, to a considerable degree overlap between Dicer-2-related (19 to 21 nt) and Dicer-2-unrelated vsRNAs, suggesting a common origin for these profiles. We found a degenerate motif significantly enriched at the cut sites of vsRNAs of various lengths which link an unknown RNase to the origins of vsRNAs biogenesis and distribution. Accordingly, the indicated RNase activity may be an important early factor for the host's antiviral defense in Lepidoptera. Central to the defense of insects against RNA viruses is the triggering of the so-called exogenous RNA interference pathway (exo-RNAi), by which viral double-stranded RNA (dsRNA) is cleaved intracellularly into viral small interfering RNAs (siRNAs) that in turn silence homologous transcripts (1). It is established that Dicer-2, a cytoplasmic RNase III class enzyme, recognizes and cuts successively the dsRNA template to produce small interfering RNA duplexes of ϳ21 nucleotides (nt) characterized by a signature of 2-nt 3=-hydroxyl overhangs (2). These duplexes are subsequently incorporated into the effector complex RISC (RNA-induced silencing complex) via interactions with Argonaute-2, which, upon discarding one of the two strands (passenger strand), is followed by selection and cleavage of viral sequences bearing perfect complementarity to the remaining strand (guide strand) (1, 3). Dicer-2 may act upon the genome of the virus itself-as in the case of dsRNA viruses-and/or on viral replication and transcription intermediates, although structured, single-stranded RNA (ssRNA) may also be utilized (4). Interestingly, several deepsequencing data have revealed that approximately 18-to 30-nt viral small RNAs (vsRNAs) of infected insects are not evenly distributed along the genomes but map preferentially in distinct genomic areas (hot spots) versus genomic stretches with unmapped or less-mapped vsRNAs (cold spots) (4-13). The origin of these profiles, as well as the hypothetical functional distinction between vsRNAs deriving from hot or cold spots, remains substantially elusive, although hot spots near the end of the genome have been attributed to structured regulatory viral regions (14) and an RNAi decoy-like mechanism driven by abundant vsRNAs ...

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“…In addition, our previous work in breast cancer showed that isomiRs can better distinguish normal breast tissue from BRCA tumors by comparison with archetype miRNAs (35). A potential explanation for the higher predictive value of isomiRs can be that quantification and modeling at the miRNA arm level inherently discards information, which can be rooted in biological mechanisms that may specifically affect isomiR levels (62)(63)(64).…”

Section: Discussionmentioning

confidence: 99%

The presence or absence alone of miRNA isoforms (isomiRs) successfully discriminate amongst the 32 TCGA cancer types

Telonis

Magee

Loher

et al. 2016

Preprint

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Previously, we demonstrated that miRNA isoforms (isomiRs) are constitutive and their expression profiles depend on tissue, tissue state, and disease subtype. We have now extended our isomiR studies to The Cancer Genome Atlas (TCGA) repository. Specifically, we studied whether isomiR profiles can distinguish amongst the 32 cancers. We analyzed 10,271 datasets from 32 cancers and found 7,466 isomiRs from 807 miRNA hairpin-arms to be expressed above threshold.Using the top 20% most abundant isomiRs, we built a classifier that relied on "binary" isomiR profiles: isomiRs were simply represented as 'present' or 'absent' and, unlike previous methods, all knowledge about their expression levels was ignored. The classifier could label tumor samples with an average sensitivity of 93% and a False Discovery Rate of 3%. Notably, its ability to classify well persisted even when we reduced the set of used features (=isomiRs) by a factor of 10. A counterintuitive finding of our analysis is that the isomiRs and miRNA loci with the highest ability to classify tumors are not the ones that have been attracting the most research attention in the miRNA field. Our results provide a framework in which to study cancer-type-specific isomiRs and explore their potential uses as cancer biomarkers

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Sequence Features of Drosha and Dicer Cleavage Sites Affect the Complexity of IsomiRs

Cited by 49 publications

References 50 publications

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes

Viral Small-RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection

The presence or absence alone of miRNA isoforms (isomiRs) successfully discriminate amongst the 32 TCGA cancer types

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