scholarly journals C. elegans “reads” bacterial non-coding RNAs to learn pathogenic avoidance

2020 ◽  
Author(s):  
Rachel Kaletsky ◽  
Rebecca S. Moore ◽  
Geoffrey D. Vrla ◽  
Lance L. Parsons ◽  
Zemer Gitai ◽  
...  
Keyword(s):  
Small Rnas ◽  
Food Sources ◽  
C Elegans ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Microbial Environment ◽  
Bacterial Small Rna ◽  
Necessary And Sufficient ◽  
Pathogen Avoidance ◽  
Dependent Mechanism

AbstractC. elegans is exposed to many different bacteria in its environment, and must distinguish pathogenic from nutritious bacterial food sources. Here, we show that a single exposure to purified small RNAs isolated from pathogenic Pseudomonas aeruginosa (PA14) is sufficient to induce pathogen avoidance, both in the treated animals and in four subsequent generations of progeny. The RNA interference and piRNA pathways, the germline, and the ASI neuron are required for bacterial small RNA-induced avoidance behavior and transgenerational inheritance. A single non-coding RNA, P11, is both necessary and sufficient to convey learned avoidance of PA14, and its C. elegans target, maco-1, is required for avoidance. A natural microbiome Pseudomonas isolate, GRb0427, can induce avoidance via its small RNAs, and the wild C. elegans strain JU1580 responds similarly to bacterial sRNA. Our results suggest that this ncRNA-dependent mechanism evolved to survey the worm’s microbial environment, use this information to make appropriate behavioral decisions, and pass this information on to its progeny.

scholarly journals E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans

2014 ◽  
Author(s):  
Alper Akay ◽  
Peter Sarkies ◽  
Eric Alexander Miska
Keyword(s):  
Small Rnas ◽  
Biological Function ◽  
Rapid Development ◽  
Rnai Pathway ◽  
Regulate Gene Expression ◽  
Double Stranded Rna ◽  
E Coli ◽  
C Elegans ◽  
Non Coding Rna ◽  
Rnai Response

The discovery of RNA interference (RNAi) in C. elegans has had a major impact on scientific research, led to the rapid development of RNAi tools and has inspired RNA-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded RNA (dsRNA) from their environment to elicit RNAi; the biological function of this mechanism is unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate gene expression in C. elegans when E. coli is offered as food. This was surprising given that C. elegans is unlikely to encounter E. coli in nature. To directly test the hypothesis that the E. coli OxyS non-coding RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C. elegans after feeding with bacteria. We clearly demonstrate that the OxyS non-coding RNA does not trigger an RNAi response in C. elegans. We conclude that the biology of environmental RNAi remains to be discovered.

scholarly journals Horizontal and vertical transmission of transgenerational memories via the Cer1 transposon

2020 ◽  
Author(s):  
Rebecca S. Moore ◽  
Rachel Kaletsky ◽  
Chen Lesnik ◽  
Vanessa Cota ◽  
Edith Blackman ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Vertical Transmission ◽  
Small Rna ◽  
Small Rnas ◽  
C Elegans ◽  
Common Pathogen ◽  
Transmission Of Information ◽  
Genomic Element ◽  
Pathogen Avoidance

AbstractAnimals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. Previously, we discovered that C. elegans protects itself from pathogens by “reading” bacterial small RNAs and using this information to both induce avoidance and transmit memories for several generations. Here we found that these memories can be transferred to naïve animals via Cer1 retrotransposon-encoded capsids. Cer1 functions at the step of transmission of information from the germline to neurons, and is required for C. elegans’ learned avoidance ability and for mothers to pass this information on to progeny. The presence of the Cer1 retrotransposon in wild C. elegans strains correlates with the ability to learn and inherit small RNA-induced pathogen avoidance. Together, these results suggest that C. elegans has co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.

How to find small non-coding RNAs in bacteria

2005 ◽  
Vol 386 (12) ◽  
pp. 1219-1238 ◽  
Author(s):  
Jörg Vogel ◽  
Cynthia Mira Sharma
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Molecules ◽  
Regulatory Circuit ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Response To Stress ◽  
Non Coding Rnas

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

scholarly journals Global Survey of miRNAs and tRNA-derived Small RNAs From Human Parasitic Protist Trichomonas Vaginalis

2020 ◽  
Author(s):  
Zhensheng Wang ◽  
Hongchang Zhou ◽  
Chunyan Wei ◽  
Zhihua Wang ◽  
Xiao Hao ◽  
...  
Keyword(s):  
Small Rnas ◽  
Trichomonas Vaginalis ◽  
Stem Loop ◽  
Sexually Transmitted ◽  
Site Analysis ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Parasitic Protist ◽  
Non Coding Rnas ◽  
Trna Halves

Abstract BackgroundSmall non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis (T. vaginalis), the causative agent of human sexually transmitted trichomoniasis, still remain to be unveiled. MethodsSmall RNA transcriptomes from Trichomonas trophozoites were deeply sequenced through Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas miRNAs and tRNA-derived small RNAs (tsRNAs). The tsRNAs candidates were confirmed by stem-loop RT-PCR and motifs to guide the cleavage of tsRNAs were predicted by performing GLAM2 algorithm. ResultsThe miRNAs were found at extremely low abundance (0.0046%) in T. vaginalis. Three categories of endogenous Trichomonas tsRNAs were identified as 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with 5'tritsRNAs dominating (67.63%) in tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRFs and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. This proved the expression of tRFs and tRNA-halves in T. vaginalis transcriptome. ConclusionsThis is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was hardly discovered. These results might promote the further research to better understand the evolution of small non-coding RNA in T. vaginalis and their functions in pathogenesis of trichomoniasis.

scholarly journals A novel binary k-mer approach for classification of coding and non-coding RNAs across diverse species

2021 ◽  
Author(s):  
Neha Periwal ◽  
Priya Sharma ◽  
Pooja Arora ◽  
Saurabh Pandey ◽  
Baljeet Kaur ◽  
...  
Keyword(s):  
Performance Metrics ◽  
Binary Sequences ◽  
C Elegans ◽  
Diverse Species ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Binary Approach ◽  
Non Coding Rnas ◽  
Nearest Neighbour Classifier

Classification among coding (CDS) and non-coding RNA (ncRNA) sequences is a challenge and several machine learning models have been developed for the same. Since the frequency of curated coding sequences is many-folds as compared to that of the ncRNAs, we devised a novel approach to work with the complete datasets from fifteen diverse species. In our proposed novel binary approach, we replaced all the A,T with 0 and G,C with 1 to obtain a binary form of coding and ncRNAs. The k-mer analysis of these binary sequences revealed that the frequency of binary patterns among the coding and ncRNAs can be used as features to distinguish among them. Using insights from these distinguishing frequencies, we used k-nearest neighbour classifier to classify among them. Our strategy is not only time-efficient but leads to significantly increased performance metrics including Matthews correlation coefficient (MCC) for some species like P. paniscus, M. mulatta, M. lucifugus, G. gallus, C. japonica, C. abingdonii, A. carolinensis, D. melanogaster and C. elegans when compared with the conventional ATGC approach. Additionally, we also show that the values of MCC obtained for diverse species tested on the model based on H. sapiens correlated with the geological evolutionary timeline thereby further strengthening our approach. Therefore, we propose that CDS and ncRNAs can be efficiently classified using 2-character frequency as compared to 4-character frequency of ATGC approach. Thus, our highly efficient binary approach can replace the more complex ATGC approach successfully.

scholarly journals Germline inherited small RNAs clear untranslated maternal mRNAs in C. elegans embryos

2020 ◽  
Author(s):  
Piergiuseppe Quarato ◽  
Meetali Singh ◽  
Eric Cornes ◽  
Blaise Li ◽  
Loan Bourdon ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Embryonic Development ◽  
Small Rnas ◽  
Dependent Manner ◽  
C Elegans ◽  
Mrna Targets ◽  
Maternal To Zygotic Transition ◽  
Catalytically Active ◽  
Maternal Mrnas ◽  
Non Coding Rnas

ABSTRACTInheritance and clearance of maternal mRNAs are two of the most critical events required for animal early embryonic development. However, the mechanisms regulating this process are still largely unknown. Here, we show that together with maternal mRNAs, C. elegans embryos inherit a complementary pool of small non-coding RNAs capable of triggering the cleavage and removal of hundreds of maternal mRNAs. These antisense small RNAs are loaded into the maternal catalytically-active Argonaute CSR-1 and cleave complementary mRNAs no longer engaged in translation in somatic blastomeres. Induced depletion of CSR-1 specifically during embryonic development leads to embryonic lethality in a slicer-dependent manner and impairs the degradation of CSR-1 embryonic mRNA targets. Given the conservation of Argonaute catalytic activity, we propose that a similar mechanism operates to clear maternal mRNAs during the maternal-to-zygotic transition across species.

scholarly journals Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Piergiuseppe Quarato ◽  
Meetali Singh ◽  
Eric Cornes ◽  
Blaise Li ◽  
Loan Bourdon ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Embryonic Development ◽  
Small Rnas ◽  
Dependent Manner ◽  
C Elegans ◽  
Mrna Targets ◽  
Maternal To Zygotic Transition ◽  
Catalytically Active ◽  
Maternal Mrnas ◽  
Non Coding Rnas

AbstractInheritance and clearance of maternal mRNAs are two of the most critical events required for animal early embryonic development. However, the mechanisms regulating this process are still largely unknown. Here, we show that together with maternal mRNAs,C. elegansembryos inherit a complementary pool of small non-coding RNAs that facilitate the cleavage and removal of hundreds of maternal mRNAs. These antisense small RNAs are loaded into the maternal catalytically-active Argonaute CSR-1 and cleave complementary mRNAs no longer engaged in translation in somatic blastomeres. Induced depletion of CSR-1 specifically during embryonic development leads to embryonic lethality in a slicer-dependent manner and impairs the degradation of CSR-1 embryonic mRNA targets. Given the conservation of Argonaute catalytic activity, we propose that a similar mechanism operates to clear maternal mRNAs during the maternal-to-zygotic transition across species.

scholarly journals A membrane-associated condensate drives paternal epigenetic inheritance in C. elegans

2020 ◽  
Author(s):  
Jan Schreier ◽  
Sabrina Dietz ◽  
Antonio M. de Jesus Domingues ◽  
Ann-Sophie Seistrup ◽  
Dieu An H. Nguyen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Small Rnas ◽  
Maternal Inheritance ◽  
Epigenetic Inheritance ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Regulatory Information ◽  
Intrinsically Disordered Region ◽  
Gene Regulatory ◽  
Non Coding Rnas

SUMMARYTransgenerational epigenetic inheritance (TEI) describes the transmission of gene-regulatory information across generations without altering DNA sequences, and allows priming of offspring towards transposable elements (TEs) and changing environmental conditions. One important mechanism that acts in TEI is based on small non-coding RNAs. Whereas factors for maternal inheritance of small RNAs have been identified, paternal inheritance is poorly understood, as much of the cellular content is extruded during spermatogenesis. We identify a phase separation-based mechanism, driven by the protein PEI-1, which is characterized by a BTB-BACK domain and an intrinsically disordered region (IDR). PEI-1 specifically secures the Argonaute protein WAGO-3 within maturing sperm in C. elegans. Localization of PEI granules in mature sperm is coupled, via S-palmitoylation, to myosin-driven transport of membranous organelles. pei-1-like genes are also found in human and often expressed in testis, suggesting that the here identified mechanism may be broadly conserved.

scholarly journals Bioinformatics Analysis of Long Non-coding RNA and Related Diseases: An Overview

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuxin Gong ◽  
Wen Zhu ◽  
Meili Sun ◽  
Lei Shi
Keyword(s):  
Small Rnas ◽  
Bioinformatics Analysis ◽  
Regulation Of Gene Expression ◽  
Research Progress ◽  
Biological Processes ◽  
Existing Problems ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Cancer Côlon ◽  
Long Non Coding Rna

Long non-coding RNAs (lncRNAs) are usually located in the nucleus and cytoplasm of cells. The transcripts of lncRNAs are >200 nucleotides in length and do not encode proteins. Compared with small RNAs, lncRNAs have longer sequences, more complex spatial structures, and more diverse and complex mechanisms involved in the regulation of gene expression. LncRNAs are widely involved in the biological processes of cells, and in the occurrence and development of many human diseases. Many studies have shown that lncRNAs can induce the occurrence of diseases, and some lncRNAs undergo specific changes in tumor cells. Research into the roles of lncRNAs has covered the diagnosis of, for example, cardiovascular, cerebrovascular, and central nervous system diseases. The bioinformatics of lncRNAs has gradually become a research hotspot and has led to the discovery of a large number of lncRNAs and associated biological functions, and lncRNA databases and recognition models have been developed. In this review, the research progress of lncRNAs is discussed, and lncRNA-related databases and the mechanisms and modes of action of lncRNAs are described. In addition, disease-related lncRNA methods and the relationships between lncRNAs and human lung adenocarcinoma, rectal cancer, colon cancer, heart disease, and diabetes are discussed. Finally, the significance and existing problems of lncRNA research are considered.

scholarly journals Emerging Functions for snoRNAs and snoRNA-Derived Fragments

2021 ◽  
Vol 22 (19) ◽  
pp. 10193
Author(s):  
Maliha Wajahat ◽  
Cameron Peter Bracken ◽  
Ayla Orang
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Biological Significance ◽  
Specific Interactions ◽  
Additional Source ◽  
Widespread Implementation ◽  
Non Coding Rna ◽  
Complex Picture ◽  
Non Coding Rnas

The widespread implementation of mass sequencing has revealed a diverse landscape of small RNAs derived from larger precursors. Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples of the production of such fragments being conserved across species. Coupled with specific interactions to RNA-binding proteins and a growing number of experimentally reported examples suggesting function, a case is emerging whereby the biological significance of small non-coding RNAs extends far beyond miRNAs and piRNAs. Related to this, a similarly complex picture is emerging of non-canonical roles for the non-coding precursors, such as for snoRNAs that are also implicated in such areas as the silencing of gene expression and the regulation of alternative splicing. This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators. This review seeks to highlight emerging roles for such non-coding RNA, focusing specifically on “new” roles for snoRNAs and the small fragments derived from them.

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