<scp>RNA</scp>‐based regulation of transposon expression

Gebert, Daniel; Rosenkranz, David

doi:10.1002/wrna.1310

Cited by 35 publications

(33 citation statements)

References 200 publications

(226 reference statements)

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“…2). This is consistent with most models of endo-siRNA and piRNA biogenesis in bilaterians in which some endo-siRNAs are cleaved from secondarily structured primary transcripts while piRNAs are not [53]. Given that the putative piRNA and endo-siRNA clusters identified here have proven to be consistent with previously reported properties, we deemed our method to be satis-factory for naive identification and annotation.…”

Section: Discrimination and Annotation Of Rnai Classes In Drosophilasupporting

confidence: 88%

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Diverse RNA interference strategies in early-branching metazoans

Calcino

Taft

Degnan

2018

Preprint

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Background: Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians -sponges, ctenophores, placozoans and cnidarians -appears to be more diverse than that of bilaterians, and includes structurally variable miR-NAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. Results:Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. In the ctenophore, the absence of miRNAs is confirmed and an abundance of endo-siRNAs is revealed. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. Conclusion:Together, these findings suggest that the last common ancestor of animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs. ABSTRACT 2 BACKGROUND RNA interference (RNAi) evolved prior to the divergence of extant eukaryotic lineages, possibly in response to threats from parasitic double-stranded RNA species such as retroviruses and transposons [1]. In contemporary animals, three independent RNAi systems comprise the bulk of the small RNA (sRNA) repertoire: micro RNAs (miRNAs); Piwi interacting RNAs (piRNAs); and endogenous small interfering RNAs (endo-siRNAs). Amongst non-bilaterian animals -sponges, cnidarians ctenophores and placozoans -miRNAs appear to be lost in latter two lineages, with placozoans and ctenophores also lacking key miRNA biogenic enzymes [2][3][4]. The absence of miRNAs in the sister lineages to the animal kingdom, choanoflagellates, and fungi [2,5,6], suggests the miRNA system has been lost or evolved independently multiple times [7]. Nonetheless, animal miRNAs play fundamental roles in cell type differentiation and maintenance, and their emergence and proliferation is linked to the evolution of complex multicellularity [8]. The prevalence of miRNAs in plants and algae [9] lends further support to the hypothesis that miRNAs may be important regu...

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Section: Discrimination and Annotation Of Rnai Classes In Drosophilasupporting

confidence: 88%

“…As anticipated, multi-mapping endo-siRNAs and piRNAs derive primarily from transposons ( Fig. 1) [53,54]. In addition, we found that unique endo-siRNA clusters frequently map to exons, 5' and 3' UTRs in coding genes ( Fig.…”

Section: Discrimination and Annotation Of Rnai Classes In Drosophilasupporting

confidence: 76%

Diverse RNA interference strategies in early-branching metazoans

Calcino

Taft

Degnan

2018

Preprint

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“…Faced with the grave threat posed by active TEs, animals employ germline-expressed PIWI proteins and PIWI-interacting (pi-) RNAs to suppress TE activity on the transcriptional and post-transcriptional level, thus ensuring the transmission of intact genomes from one generation to another [24]. We have recently shown that shifts in temperature from 18 C to 29 C not only alter the expression level of specific TEs in Drosophila melanogaster, but also lead to a more pronounced PIWI/piRNA response, presumably due to reduced back folding of TE transcripts, making them more accessible for piRNAguided PIWI attacks [4].…”

Section: Ii) Temperature and Transposon Propagation In Drosophila Evomentioning

confidence: 99%

Temperature-dependent small RNA expression in Drosophila melanogaster

Fast

Rosenkranz

2018

RNA Biology

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Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures. In this commentary, we will dwell upon particular interesting aspects connected to our findings, hoping that our point of view may encourage other scientists to address some of the questions raised here. We will particularly focus on aspects related to climate-dependent transposon propagation in evolution and putative transgenerational epigenetic effects of altered small RNA transcriptomes. We further briefly indicate how temperature-responsive miRNAs may confound the interpretation of data obtained from experiments comprising heat-shock treatment which is a widely used technique not only in Drosophila genetics.

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“…Small non-coding (snc-) RNAs are important players in diverse cellular processes, often acting as guide molecules in transcriptional and post-transcriptional gene regulation [1,2,3]. Micro (mi-) RNAs, short interfering (si-) RNAs and Piwiinteracting (pi-) RNAs constitute their most prominent representatives but the number of described sncRNA classes continuously increases.…”

Section: Introductionmentioning

confidence: 99%

unitas: the universal tool for annotation of small RNAs

Gebert¹,

Hewel²,

Rosenkranz³

2017

Preprint

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Background: Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs. Results: Here we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases (currently more than 800). unitas combines high quality annotation and numerous analysis features in a user-friendly manner. A complete annotation can be started with one simple shell command, making unitas particularly useful for researchers not having access to a bioinformatics facility. Noteworthy, the algorithms implemented in unitas are on par or even outperform comparable existing tools for small RNA annotation that base on available ncRNA sequence information. Conclusions: unitas brings together annotation and analysis features that hitherto required the installation of numerous different bioinformatics tools which can pose a challenge for the non-expert user. With this, unitas overcomes the problem of read normalization. Moreover, the high quality of sequence annotation and analysis, paired with the ease of use, make unitas a valuable tool for researchers in all fields connected to small RNA biology.

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RNA‐based regulation of transposon expression

Cited by 35 publications

References 200 publications

Diverse RNA interference strategies in early-branching metazoans

Diverse RNA interference strategies in early-branching metazoans

Temperature-dependent small RNA expression in Drosophila melanogaster

unitas: the universal tool for annotation of small RNAs

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