Bacterial Argonaute samples the transcriptome to identify foreign DNA
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ABSTRACT:
PROVIDER: PRJNA215165 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR952291.fastq.gz | Fastqsanger.gz | |||
| SRR952292.fastq.gz | Fastqsanger.gz | |||
| SRR952293.fastq.gz | Fastqsanger.gz | |||
| SRR952294.fastq.gz | Fastqsanger.gz | |||
| SRR952295.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15-19 nt small RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22-24 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid–derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated, while other genes are unaffected. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids.
2013-09-12 | GSE49865 | GEO
Project description:Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15-19 nt small RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22-24 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid–derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated, while other genes are unaffected. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids. Small RNA and small DNA from purified RsAgo expressed in Rhodobacter sphaeroides ATCC17025 ("strain 25") and E. coli BL21(DE3) Total small RNA (13-30nt) from R. sphaeroides ATCC17025 and ATCC17029 (wild-type; RsAgo mutant; containing either empty or RsAgo-expressing plasmid) Total ribosomal RNA-depleted RNA from wild type or RsAgo mutant R. sphaeroides ATCC17025
2013-09-12 | E-GEOD-49865 | biostudies-arrayexpress
Project description:Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea, their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15-19 nt RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22-24 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid-derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids.
| S-EPMC3809076 | biostudies-literature
Project description:We report identification of 348 high confidence miRNA target sites in 261 genes in the bovine retina Employ Argonaute HITS-CLIP analysis to identify miRNA target sites in the bovine retina
2014-09-10 | E-GEOD-59909 | biostudies-arrayexpress
Project description:Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.
| S-EPMC5435312 | biostudies-literature
Project description:Silicone-based medical devices are widely used in chronic implants and are generally perceived to be safe. However, immune-related complications including malignancies have recently been linked to textured breast implants. Here, we examine the influence of clinically approved breast implants surface features on host immune responses. Prosthetics with surface roughness of 0, 4, and 90 (Ra) were implanted in mammary fat pads of mice for 2 weeks and cells adjacent to the resulting tissue capsules were evaluated for foreign body immune responses using single-cell RNA-seq. Our findings identify a unique and finely tuned surface topography that is capable of modulating implant immunity to suppress foreign body response.
2021-05-28 | GSE164645 | GEO
Project description:Although macrophage-epithelioid cell (EPC)-giant cell (GC) differentiation is acknowledged in foreign body reaction (FBR), the exact molecular features remain elusive. To discover the molecular profiles of EPC and GC, we analyzed mouse sponge and silk FBRs by integrating single-cell RNA-sequencing (scRNA-seq) and spatial sequencing.
2022-05-17 | GSE203165 | GEO
Project description:HEK-293-derived cell lines depleted of Dicer or one of four Argonaute proteins were generated. Microarray analysis of these knock down cell lines and various control cell lines was performed to address how large the proportion of genes is that are regulated by RNA silencing in an individual cell type. Comparison of different arrays revealed commonly (up) regulated genes. The highest overlap was observed in Ago2 and Dicer knockdown cells. Experiment Overall Design: three control cell lines (T-Rex, shRNA, empty vector), two induvidual Argonaute 1 and 4 (Ago1kd, Ago4kd) knock down cell lines, one Argonaute 2 and 3 (Ago2kd, Ago3kd) and two induvidual Dicer knock down cell lines were analyzed as biological replicates
2008-06-12 | E-GEOD-4246 | biostudies-arrayexpress
Project description:The goal of this study was to identify small RNA-ARGONAUTE interactions in Arabidopsis. Co-immunoprecipitation assays followed by high-throughput sequencing were done to identify small RNA associated with HA-AGO2 and HA-AGO7. Keywords: small RNA - ARGONAUTE interactions
2008-08-16 | GSE12037 | GEO
Project description:In many eukaryotes, Argonaute proteins, guided by short RNA sequences, defend cells against transposons and viruses. In the eubacterium Thermus thermophilus, the DNA-guided Argonaute TtAgo defends against transformation by DNA plasmids. Here, we report that TtAgo also participates in DNA replication. In vivo, TtAgo binds 15-18 nt DNA guides derived from the chromosomal region where replication terminates and associates with proteins known to act in DNA replication. When gyrase, the sole T. thermophilus type II topoisomerase, is inhibited, TtAgo allows the bacterium to finish replicating its circular genome. In contrast, loss of both gyrase and TtAgo activity slows growth and produces long sausage-like filaments in which the individual bacteria are linked by DNA. Finally, wild-type T. thermophilus outcompetes an otherwise isogenic strain lacking TtAgo. We propose that the primary role of TtAgo is to help T. thermophilus disentangle the catenated circular chromosomes generated by DNA replication.
2020-03-17 | MSV000085109 | MassIVE