ArticleBMC genomics2013
RIP-seq of BmAgo2-associated small RNAs reveal various types of small non-coding RNAs in the silkworm, Bombyx mori.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 42 citations in OpenAlex.
- Article
- Multi-omics study and ncRNA regulation of anti-BmNPV in silkworms,Frontiers in microbiology · 2023Review
- Next-generation sequencing: A new avenue to understand viral RNA-protein interactions.The Journal of biological chemistry · 2022Review
- Cytoplasmically localized tRNA-derived fragments inhibit translation inTurkish journal of biology = Turk biyoloji dergisi · 2022Article
- Improvement of host-induced gene silencing efficiency via polycistronic-tRNA-amiR expression for multiple target genes and characterization of RNAi mechanism in Mythimna separata.Plant biotechnology journal · 2021Article
- Next Generation dsRNA-Based Insect Control: Success So Far and Challenges.Frontiers in plant science · 2021Review
- Transfer RNA and Origins of RNA Interference.Frontiers in molecular biosciences · 2021Article
- On the expanding roles of tRNA fragments in modulating cell behavior.Nucleic acids research · 2020Review
- Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions.Non-coding RNA · 2019Review
- Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice.Molecular & cellular proteomics : MCP · 2018Article
- Insights into RNAi-based antiviral immunity in Lepidoptera: acute and persistent infections in Bombyx mori and Trichoplusia ni cell lines.Scientific reports · 2018Article
- Transcriptome profiling reveals infection strategy of an insect maculavirus.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti.PLoS neglected tropical diseases · 2018Article
- The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells.Nucleic acids research · 2017Article
- Transposable Element Bm1645 is a Source of BmAGO2-associated Small RNAs that affect its expression in Bombyx mori.BMC genomics · 2017Article
- tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression.Life (Basel, Switzerland) · 2015Review
- tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins.Gene regulation and systems biology · 2015Review
- Transfer RNA as a source of small functional RNA.Journal of molecular biology and molecular imagingArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSmall non-coding RNAs (ncRNAs) are important regulators of gene expression in eukaryotes. Previously, only microRNAs (miRNAs) and piRNAs have been identified in the silkworm, Bombyx mori. Furthermore, only ncRNAs (50-500nt) of intermediate size have been systematically identified in the silkworm.
resultsHere, we performed a systematic identification and analysis of small RNAs (18-50nt) associated with the Bombyx mori argonaute2 (BmAgo2) protein. Using RIP-seq, we identified various types of small ncRNAs associated with BmAGO2. These ncRNAs showed a multimodal length distribution, with three peaks at ~20nt, ~27nt and ~33nt, which included tRNA-, transposable element (TE)-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. The tRNA-derived fragments (tRFs) were found at an extremely high abundance and accounted for 69.90% of the BmAgo2-associated small RNAs. Northern blotting confirmed that many tRFs were expressed or up-regulated only in the BmNPV-infected cells, implying that the tRFs play a prominent role by binding to BmAgo2 during BmNPV infection. Additional evidence suggested that there are potential cleavage sites on the D, anti-codon and TψC loops of the tRNAs. TE-derived small RNAs and piRNAs also accounted for a significant proportion of the BmAgo2-associated small RNAs, suggesting that BmAgo2 could be involved in the maintenance of genome stability by suppressing the activities of transposons guided by these small RNAs. Finally, Northern blotting was also used to confirm the Bombyx 5.8 s rRNA-derived small RNAs, demonstrating that various novel small RNAs exist in the silkworm.
conclusionsUsing an RIP-seq method in combination with Northern blotting, we identified various types of small RNAs associated with the BmAgo2 protein, including tRNA-, TE-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. Our findings provide new clues for future functional studies of the role of small RNAs in insect development and evolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.