ArticlePLoS computational biology2005
The RNA silencing pathway: the bits and pieces that matter.
Article in PLoS computational biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 55 citations in OpenAlex.
- Biochemical and nanotechnological approaches to combat phytoparasitic nematodes.Plant biotechnology journal · 2024Review
- Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii.Nature protocols · 2024Review
- Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition.Cell systems · 2023Article
- Transcriptomics and solid tumors: The next frontier in precision cancer medicine.Seminars in cancer biology · 2022Review
- Kinetics ofJournal of drug delivery science and technology · 2021Article
- Efficient tuning of siRNA dose response by combining mixed polymer nanocarriers with simple kinetic modeling.Acta biomaterialia · 2017Article
- RNAi-mediated Control of Aflatoxins in Peanut: Method to Analyze Mycotoxin Production and Transgene Expression in the Peanut/Aspergillus Pathosystem.Journal of visualized experiments : JoVE · 2015Article
- RNAi revised--target mRNA-dependent enhancement of gene silencing.Nucleic acids research · 2015Article
- Multi-scale modeling of tissues using CompuCell3D.Methods in cell biology · 2012Article
- Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.Cell · 2011Article
- Subcellular fate and off-target effects of siRNA, shRNA, and miRNA.Pharmaceutical research · 2011Review
- Is RNA-dependent RNA polymerase essential for transposon control?BMC systems biology · 2011Article
- Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple turnover.Journal of molecular biology · 2011Article
- Optimal viral strategies for bypassing RNA silencing.Journal of the Royal Society, Interface · 2011Article
- Quantitative analysis of cellular metabolic dissipative, self-organized structures.International journal of molecular sciences · 2010Review
- Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study.BMC genomics · 2009Article
- Multicell simulations of development and disease using the CompuCell3D simulation environment.Methods in molecular biology (Clifton, N.J.) · 2009Article
- RNA silencing can explain chlorotic infection patterns on plant leaves.BMC systems biology · 2008Article
- Maintaining the silence: reflections on long-term RNAi.Drug discovery today · 2008Review
- Modeling recursive RNA interference.PLoS computational biology · 2008Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing pathway operates by cleaving siRNAs from dsRNA. siRNAs can associate with RISC, leading to the degradation of the target mRNA. We propose and analyze a few small extensions to the pathway: a siRNA degrading RNase, primed amplification of aberrant RNA pieces, and cooperation between aberrant RNA to trigger amplification. These extensions allow for a consistent explanation for various types of silencing phenomena, such as virus induced silencing, transgene and transposon induced silencing, and avoidance of self-reactivity, as well as for differences found between species groups.
Identifiers
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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.