ArticleMolecular biology reports2014
Characterizing RNA-protein interaction using cross-linking and metabolite supplemented nuclear RNA-immunoprecipitation.
Article in Molecular biology reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP).Advances in experimental medicine and biology · 2024Article
- RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks.Molecular cell · 2023Article
- The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation.The Plant cell · 2022Article
- Next-generation sequencing: A new avenue to understand viral RNA-protein interactions.The Journal of biological chemistry · 2022Review
- Towards an IdealInternational journal of molecular sciences · 2022Review
- Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA.RNA (New York, N.Y.) · 2020Article
- Impairing the function of MLCK, myosin Va or myosin Vb disrupts Rhinovirus B14 replication.Scientific reports · 2017Article
- Article
- TruSeq-Based Gene Expression Analysis of Formalin-Fixed Paraffin-Embedded (FFPE) Cutaneous T-Cell Lymphoma Samples: Subgroup Analysis Results and Elucidation of Biases from FFPE Sample Processing on the TruSeq Platform.Frontiers in medicine · 2017Article
- In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings.The Plant cell · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-immunoprecipitation (RNA-IP) is a method used to isolate and identify RNA molecules specifically associated with an RNA-binding protein. Non-coding RNAs are emerging as key regulators of many biological and developmental pathways and RNA-IP has become an important tool in studying their function(s). While RNA-IP is successfully used to determine protein-RNA interaction, specific details regarding the level of this association and the metabolic requirement of this interaction which can influence the success of RNA-IP remain unclear. Here, we investigate the conditions required for efficient nuclear RNA-IP using Arabidopsis AGO4 (Argonaute 4) and siRNA binding as the study model. We showed that formaldehyde cross-linking, but not UV cross-linking, allowed for efficient pull-down of 24-nt siRNAs, suggesting that AGO4-siRNA interaction involves other protein(s). We also showed that, while formaldehyde cross-linking could also be performed on purified nuclei, ATP supplementation to the nuclei isolation buffer was needed to efficiently pull down 24-nt siRNAs. This result indicates that ATP is required for efficient siRNA loading onto AGO4. As most of the known RNA-mediated regulatory processes occur in the nucleus, our findings on cross-linking conditions and metabolite requirement for successful AGO4 nuclear RNA-IP provide a valuable insight and future consideration when studying the function of protein-RNA interactions in plants.
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