ABSTRACT
Almost all RNAs need to interact with proteins to fully exert their functions, and proteins also bind to RNAs to act as regulators. It has now become clear that RNA-protein interactions play important roles in many biological processes among organisms. Despite the great progress that has been made in the field, there is still no precise classification system for RNA-protein interactions, which makes it challenging to further decipher the functions and mechanisms of these interactions. In this review, we propose four different categories of RNA-protein interactions according to their basic characteristics: RNA motif-dependent RNA-protein interactions, RNA structure-dependent RNA-protein interactions, RNA modification-dependent RNA-protein interactions, and RNA guide-based RNA-protein interactions. Moreover, the integration of different types of RNA-protein interactions and the regulatory factors implicated in these interactions are discussed. Furthermore, we emphasize the functional diversity of these four types of interactions in biological processes and disease development and assess emerging trends in this exciting research field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
Subject(s)
Proteins/metabolism , RNA/metabolism , Animals , HumansABSTRACT
RNA can interact with RNA-binding proteins (RBPs), mRNA, or other non-coding RNAs (ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins (RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.
Subject(s)
RNA, Messenger/chemistry , RNA, Untranslated/chemistry , RNA-Binding Proteins/chemistry , Binding Sites , Computational Biology , Gene Expression Regulation , High-Throughput Nucleotide Sequencing , Models, Molecular , Mutation/genetics , Nucleic Acid Conformation , Protein Binding , Sequence Analysis, RNA , Transcriptome/geneticsABSTRACT
BACKGROUND: Sublingual immunotherapy (SLIT) is a clinically effective treatment in allergic conjunctivitis (AC); however, the mechanism of the underlying pharmacodynamics remains unclear. Here, we investigate the efficacy and the mechanism of a sublingually administered Dermatophagoides farinae (Der f) vaccine in a murine AC model. METHODS: A murine model of AC caused by Der f extract was developed in BALB/c mice by repeated application of allergen. Sensitized mice were SLIT treated by Der f drops and subsequently analyzed for AC symptoms, histopathological and immunological parameters. RESULTS: In this study, Der f extract successfully induced the symptoms of AC in BALB/c mice. In these sensitized mice, clinical symptoms (scratching behavior, lacrimation, conjunctival hyperemia and edema), immunological and histopathological findings (inflammatory cell infiltration) were very similar to those in human AC. SLIT treatment of sensitized mice markedly reduced the clinical and histopathological symptoms and decreased the expression levels of total immunoglobulin E (IgE), Der f-specific IgE and T helper cell 2 (Th2) cytokine interleukin-4, with a significant increase in Der f-specific IgG4 and Th1 cytokine interferon-γ. CONCLUSIONS: SLIT with Der f drops is a potentially effective means of immunotherapy for Der f-induced AC by modulating the Th2-biased allergic immune response.
Subject(s)
Antigens, Dermatophagoides/therapeutic use , Arthropod Proteins/therapeutic use , Conjunctivitis, Allergic/therapy , Cysteine Endopeptidases/therapeutic use , Immunotherapy, Active , Administration, Sublingual , Animals , Anti-Allergic Agents/therapeutic use , Antigens, Dermatophagoides/immunology , Arthropod Proteins/immunology , Conjunctiva/pathology , Conjunctivitis, Allergic/immunology , Cysteine Endopeptidases/immunology , Disease Models, Animal , Down-Regulation , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunoglobulin E/blood , Interleukin-4/blood , Mice , Mice, Inbred BALB C , Th2 Cells/cytologyABSTRACT
A new di-O-prenylated flavone, named 7,3'-di-(γ,γ-dimethylallyloxy)-5-hydroxy-4'-methoxyflavone (1), was isolated from the culture broth of the endophytic actinomycete Streptomyces sp. MA-12 isolated from the root of the semi-mangrove plant Myoporum bontioides A. Gray. The structure of 1 was determined by comprehensive spectroscopic methods, including 1D and 2D NMR experiments (COSY, HMQC, and HMBC). Primary bioassays showed that 1 at concentration of 0.25 mM had moderate inhibitory activity against three plant pathogenic fungi including Colletotrichum musae, Gibberella zeae (Schweinitz) Petch, and Penicillium citrinum Thom.
