Ontology highlight
ABSTRACT:
PROVIDER: PRJNA708299 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13913548.fastq.gz | Fastqsanger.gz | |||
| SRR13913549.fastq.gz | Fastqsanger.gz | |||
| SRR13913550.fastq.gz | Fastqsanger.gz | |||
| SRR13913551.fastq.gz | Fastqsanger.gz | |||
| SRR13913552.fastq.gz | Fastqsanger.gz |
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Project description:Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes (Lm) expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned RNA (<500nt) isolated from extracellularly growing bacteria and from Lm-infected macrophages to catalog the sRNA repertoire during intracellular bacterial growth. Here we report on the discovery of 150 regulatory RNAs of which 71 have never been previously described. A total of 29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly. We validated highly expressed sRNAs by Northern blotting and demonstrated by the construction and characterization of isogenic mutants of rli31, rli33-1 and rli50 for intracellular expressed sRNA candidates, that their expression is required for efficient growth of bacteria in macrophages. All three mutants were attenuated when assessed for growth in mouse and insect models of infection. Comparative genomic analysis revealed the presence of lineage specific sRNAs and the absence of sRNA loci in genomes of naturally-occurring infection-attenuated bacteria, with additional loss in non-pathogenic listerial genomes. Our analyses reveal extensive sRNA expression as an important feature of bacterial regulation during intracellular growth.
2011-07-21 | E-MTAB-329 | biostudies-arrayexpress
Project description:PIWI-interacting RNAs (piRNAs) promote fertility in many animals. Yet, whether this is due to their conserved role in repressing repetitive elements (REs) or other functions remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets, but rather mediated by the epigenetic silencing of all the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway is sufficient to restore histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that the transgenerational silencing of histone genes contributes to the progressive loss of fertility in piRNA mutants and that coupling piRNAs and histone silencing may serve to maintain piRNAs production across evolution.
2019-12-11 | PXD012557 | Pride
Project description:Due to low numbers and poor accessibility of host cells that are targeted for effector delivery, the actual biological functions of most effectors remain elusive. Here, we developed a novel Isolation Nuclei TArgeted by Bacterial Effectors (INTABE) system, which facilitates selectively recovering nuclei of the cells in Arabidopsis thaliana plants that have received type-III effectors of pathogenic Xanthomonas bacteria. Using these nuclei as studying materials, we analysed changes in host gene expression and their correlation with changes in DNA methylation induced by Xanthomonas effector Outer Protein D (XopD).
2022-10-22 | E-MTAB-10281 | biostudies-arrayexpress
Project description:Humans and microorganisms, both symbiotic and pathogenic, have evolved means to communicate through the dissemination of biological signals. In addition to small molecules and proteins, mobile small RNAs (sRNAs) have recently emerged as signal molecules that mediate inter-species crosstalk by functional RNA interference (RNAi). However, the trafficking of sRNAs between humans and microorganisms, as well as the resulting biological consequences, remains unexplored. Here, we report that human cells secrete exosomes to deliver sRNAs into bacteria and induce bacterial gene silencing. The unprecedented RNAi in bacteria is accomplished primarily through translational repression without mRNA degradation, for which the participation of human AGO2 proteins co-transferred with sRNAs is essential. Exosome-mediated bacterial RNAi was further applied to fight superbug infection by targeting drug-resistance genes in a mouse model. Our discovery of this unique exosome-mediated sRNA delivery and gene silencing in bacteria paves the way to understanding and manipulating the cross-kingdom communication between human hosts and intestinal microbiota, as well as between humans and pathogenic bacteria.
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Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
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2022-10-22 | E-MTAB-10280 | biostudies-arrayexpress
Project description:Organisms can develop adaptive sequence-specific immunity by reexpressing pathogen-specific small RNAs that guide gene silencing. For example, the C. elegans PIWI-Argonaute/piwi-interacting RNA (piRNA) pathway recruits RNA-dependent RNA polymerase (RdRP) to foreign sequences to amplify a transgenerational small-RNA-induced epigenetic silencing signal (termed RNAe). Here, we provide evidence that, in addition to an adaptive memory of silenced sequences, C. elegans can also develop an opposing adaptive memory of expressed/self-mRNAs. We refer to this mechanism, which can prevent or reverse RNAe, as RNA-induced epigenetic gene activation (RNAa). We show that CSR-1, which engages RdRP-amplified small RNAs complementary to germline-expressed mRNAs, is required for RNAa. We show that a transgene with RNAa activity also exhibits accumulation of cognate CSR-1 small RNAs. Our findings suggest that C. elegans adaptively acquires and maintains a transgenerational CSR-1 memory that recognizes and protects self-mRNAs, allowing piRNAs to recognize foreign sequences innately, without the need for prior exposure.
2013-12-23 | GSE49532 | GEO
Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
2016-03-17 | GSE75281 | GEO
Project description:We present the first genome-wide identification and characterizaion of 422 novel sRNAs in R. capsulatus. In addition we report a comparative analysis of conserved sRNAs across 24 bacterial species.
2017-04-05 | GSE82056 | GEO
Project description:Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNA interference phenotypes in C. elegans provides an excellent model to study this phenomenon, and whilst studies have implicated both chromatin modifications and small RNA pathways in heritable silencing their relative contributions remain unclear. Here we demonstrate that the histone methyltransferases SET-25 and SET-32 are required for the establishment of a transgenerational silencing signal, but not for long-term maintenance of this signal between subsequent generations suggesting that transgenerational epigenetic inheritance is a multi-step process, with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNA (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
2018-10-30 | PXD008754 | Pride