56 results about "RNA-Binding Motif" patented technology

This invention discloses a method and system for predicting RNA binding protein binding sites on RNA without targeting, relating to the field of bioinformatics. The method includes the following steps: acquiring raw RNA structure data; expanding and filtering the preprocessed data; training an RNA analysis model using the filtered data; processing the RNA to be analyzed using the trained RNA analysis model, calculating the probability that each nucleotide is single-stranded, and obtaining a structure score; identifying low-accessibility regions based on the difference between the structure score output by the RNA analysis model and the structure score calculated by the original method; and identifying potential RNA binding protein binding sites by comparing the signal difference with that of the original method in a single RNA structure detection experiment. This invention utilizes the STONE method to improve the accuracy of RNA structure analysis in low-accessibility regions, and uses the improved difference to infer RBP binding sites, thereby improving the accuracy of RBP binding site identification.

According to the RNA binding protein HuR inhibitor and the anti-fibrosis application thereof, the compound provided by the invention has obvious inhibitory activity on HuR protein, has a good anti-renal fibrosis effect, can obviously reduce protein and mRNA expression levels of fibronectin (FN1) and alpha-smooth muscle actin (alpha-SMA), can improve renal function impairment, and can be used for preparing the anti-fibrosis medicine for treating renal fibrosis. The levels of blood urea nitrogen (BUN) and creatinine (Cr) which are commonly used for evaluating the renal function are reduced, and the compound can be used for preparing the medicine for treating the chronic kidney disease.

The present application provides a kind of brown planthopper RNA binding protein NlRBP gene inhibitor and application, the NlRBP gene inhibitor is the dsRNA capable of inhibiting brown planthopper NlRBP gene expression, the nucleotide sequence of the dsRNA is as shown in SEQ ID NO.3.The present application also provides the application of the above-mentioned brown planthopper RNA binding protein NlRBP gene inhibitor in the prevention and treatment of brown planthopper.The prevention and treatment of brown planthopper is to inhibit the survival rate of brown planthopper.The survival rate of brown planthopper is realized by inhibiting the expression of brown planthopper RNA binding protein NlRBP gene.The present application also provides the application of the above-mentioned dsRNA in preparation product.The present application provides a new prevention and treatment strategy and target for brown planthopper prevention and treatment, establishes the technology based on RNAi green control brown planthopper, provides foundation and reference for the precision, sustained pest control of brown planthopper, and has good application prospect.

Disclosed are methods, systems, and computer readable media for predicting interactions for RNA sequences, including long noncoding RNA (IncRNA), which can be used, for example, as biomarkers. In an example method of predicting one or more binding sites between a ribonucleotide (RNA) sequence and a RNA binding protein, the method includes at a computing platform including at least one processor and memory: preparing sequence data for a plurality of overlapping RNA segments derived from a target sequence; inputting the sequence data for the plurality of overlapping RNA segments into a machine learning model trained to predict a probability of an interaction between a RNA sequence and a RNA binding protein occurring in a RNA sequence; outputting from the machine learning model one or more segments in the sequence data for the plurality of overlapping RNA segments falling above a probability threshold indicative of a region of interaction between a RNA sequence and a RNA binding protein; and predicting one or more binding sites between a RNA sequence and a RNA binding protein in the sequence data for the plurality of overlapping RNA segments derived from the target sequence based on the output from the model.

The present invention includes compounds and compositions, and methods of use thereof for modulating an RNA transcript, or a precursor, isoform, fragment, or mutant thereof by degradation of the RNA transcript via recruitment or binding of one or more decay factors (e.g., an RNA binding protein).

The present application provides a fusion protein comprising an anti-CD3 single-domain antibody, an exosome protein CD63 and an RNA binding protein, and uses thereof. The fusion protein of the present application achieves the effects of treating cancer, immune regulation and activating immune cells through various efficacy experiments.

This invention discloses a novel application of the RNA-binding protein HNRNPA1 in regulating copper death in synovial fibroblasts of rheumatoid arthritis (RA-FLS). Overexpression of HNRNPA1 recognizes and binds to the m6A modification site of SLC3A2 mRNA, enhancing its transcript stability, restoring the expression of SLC3A2 and copper death-related proteins, reducing MDA levels, increasing copper ion concentration and the activity of antioxidant enzymes SOD and POD, thereby repairing mitochondrial ultrastructural damage, inhibiting abnormal cell proliferation, and inducing apoptosis. Reversal experiments confirmed that knocking down SLC3A2 reverses the above effects, indicating that SLC3A2 is a core downstream target of HNRNPA1-mediated copper death. This invention reveals for the first time the decisive role of the HNRNPA1-SLC3A2-copper death axis in the pathological phenotype of RA-FLS, providing a new target for molecular intervention in rheumatoid arthritis.

The present invention includes compounds and compositions, and methods of use thereof for modulating an RNA transcript, or a precursor, isoform, fragment, or mutant thereof by degradation of the RNA transcript via recruitment or binding of one or more decay factors (e.g., an RNA binding protein).

The present disclosure provides methods for simultaneously identifying dynamic and disease- relevant RNA binding protein (RBP)-RNA interaction (PRI) sites throughout the transcriptome at single-nucleotide resolution. The methods disclosed herein recapitulate the PRI profiles obtained with several different conventional PRI methods with several orders of magnitude improvement in efficiency in a single assay and allow identification of the specific RBP bound at the PRI.

The invention belongs to the technical field of biological genes, and discloses a method for identifying RNA interaction protein based on a Turbo ID technology and an MCP / MS2 system, the method can be used for identifying protein interacting with RNA in vitro or in vivo, and the method specifically comprises the following steps: firstly, respectively constructing RNA expression vectors inserted with MS2 tags, then constructing fusion protein vectors expressing MCP-Turbo ID, and finally constructing fusion protein vectors for expressing MCP-Turbo ID; the method comprises the following steps of: inserting RNA (Ribonucleic Acid) into an MS2 tag, transgenosis into a plant receptor by utilizing an agrobacterium tumefaciens mediated genetic transformation method to obtain a transgenic plant material expressing MCP-Turbo ID, combining the RNA inserted with the MS2 tag with the MCP-Turbo ID in vivo / in vitro by utilizing a hybridization or in-vitro incubation method, further enabling the Turbo ID to be adjacent to the RNA, biotinylating the RNA binding protein, and obtaining a transgenic plant material expressing the MCP-Turbo ID. And then enriching biotinylated protein by adopting streptavidin magnetic beads, and identifying and analyzing through Western Blot and mass spectrometry. The method not only solves the problem that the interaction protein of specific RNA in a living cell environment cannot be effectively identified in the prior art, but also can capture a transient or low-affinity RNA-protein interaction relationship.

The application discloses a kind of targeted exosome chimeric antigen receptor molecules for treating HIV infection and its application, belong to the field of biological medicine technology.The application is packaged into targeted exosome by coding anti-HIV CAR mRNA directionally.The nano antibody sequence of targeted CD3, CD4, CD8+T receptor on T cell is fused to the N-terminal of LAMP-2B to construct specific targeting plasmid, so that the targeted peptide is expressed on the surface of exosome membrane, the expression plasmid containing RNA binding protein L7A and exosome tag protein CD63 is constructed, and the exosome loaded with CAR mRNA and targeted to T cell is obtained by three-plasmid co-transfection of HEK293F cells containing C / D box CAR plasmid.The exosome can construct human CAR-T cell when incubated with PBMC in vitro or back into humanized mouse in vivo, and has significant killing virus infected cell activity.

Provided are compositions and methods for attenuating YTHDF1 activity, as well as compositions and methods for promoting an immune response. For example, provided is a YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) attenuating agent, wherein the attenuating agent comprises a compound that, when bound to YTHDF1, binds to at least one residue of YTHDF1.

We described herein are click edits, which are a series of genome editing methods that combine DNA nicking enzymes, including but not limited to RNA programmable CRISPR nicking enzymes, with DNA ligases or DNA polymerases to perform many different genome edits. Edits of interest are encoded on nucleic acid templates or substrates (optionally'click nucleic acids' (clkNA) or'click DNA '(clkDNA) as described herein) that can be provided in trans form or recruited preferentially to a target site via a variety of nucleic acid telomere methods (optionally HUH family endonucleases (HUHe), telomere binding proteins (TBP), or DNA binding proteins or RNA binding proteins).

A method for designing a protein capable of binding in an RNA base selective manner or RNA base sequence specific manner is provided. The protein of the present invention is a protein containing one or more of PPR motifs (preferably 2 to 14 PPR motifs) each consisting of a polypeptide of 30- to 38-amino acid length represented by the formula 1 (wherein Helix A is a moiety of 12-amino acid length capable of forming an α-helix structure, and is represented by the formula 2, wherein, in the formula 2, A1 to A12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3, wherein, in the formula 3, the amino acids are numbered “i” (−1), “ii” (−2), and so on from the C-terminus side, provided that Liii to Lvii may not exist), and combination of three amino acids A1, A4 and Lii, or combination of two amino acids A4, and Lii is a combination corresponding to a target RNA base or base sequence.

The invention discloses a two-step immobilization and step-by-step separation method of an RNA-protein compound, and belongs to the field of analytical chemistry. The protein is crosslinked by utilizing the characteristic that N-hydroxysuccinimide ester (NHS) structures at two ends of a DSP (Digital Signal Processor) structure react with amino groups of the protein, and the complete RPC is enriched and captured from living cells by utilizing the characteristic that 254nm crosslinked RNA and a Psoralen probe capture RNA and are compatible with M-280 magnetic beads. And respectively eluting the RNA indirect binding protein and the RNA direct binding protein which form the RNA-protein compound by utilizing the property that the TCEP breaks the disulfide bond, so as to carry out proteomics mass spectrometry analysis on the RNA binding protein in the RNA-protein compound.

The invention discloses application of salvianolic acid C in preparation of a medicine for preventing and / or treating retinal ischemia hypoxic nerve injury diseases, and relates to the technical field of biological medicines. The invention proposes and verifies for the first time that salvianolic acid C can significantly promote the formation of stress particles in photoreceptor cells under retinal ischemia and hypoxia conditions, and drives the salvianolic acid C to be assembled into a stress particle-mitochondrial micro-region in a mitochondrial adjacent region. The microcell is enriched in DDX3X, LARP1 and other key RNA binding proteins and multiple mitochondrial related proteins to cooperatively maintain mitochondrial membrane potential, inhibit mPTP opening and reduce ROS generation, so that an endogenous apoptosis pathway is inhibited, and the neuroprotective effect on a photoreceptor is achieved. On the basis, the salvianolic acid C is used for preparing the medicine for preventing and / or treating the retinal ischemia hypoxia nerve injury disease, can be used as a nerve protection supplement for existing anti-VEGF treatment, and has innovativeness and application value.

The invention specifically discloses application of RNA binding protein FXR1 as a target spot in preparation of products for preventing and treating metabolism-related fatty liver diseases and improving glucose and lipid metabolism disorders, and relates to the technical field of biological medicines. By constructing a liver specific knockout mouse (HKO) and high-fat and high-sugar diet induction model, the invention reveals that the RNA binding protein FXR1 is a key pathogenic factor for liver fatty degeneration and metabolic disorder for the first time, and discovers that the deletion of the RNA binding protein FXR1 can significantly improve liver lipid deposition, alleviate liver injury and fibrosis, and can be used for treating liver fatty degeneration and metabolic disorder. The invention can improve the abnormal glucose tolerance and insulin resistance of the whole body, and inhibit the RNA binding protein FXR1 as a new strategy for treating liver glycolipid metabolism and metabolism-related fatty liver diseases.

The application discloses a method for predicting the binding site of RNA binding protein and circular RNA, which comprises the following steps: firstly, expanding the shallow features in the network in a multi-scale manner, then expanding the deep features by decoding the features before entering the recurrent neural network, then sending the expanded deep and shallow features into the full connection layer of the classification network for classification after fusing the deep and shallow features, and finally judging whether it is a binding site according to the classification result, so as to realize the prediction of the binding site of RNA binding protein and circular RNA; the method extracts and expands the information of different levels, sends the expanded deep and shallow features into the classification network after fusing the deep and shallow features, finally judges whether it is a binding site, and through multi-branch learning, the feature expansion is carried out in stages, the information is extracted twice, and the prediction accuracy of the binding site of RNA binding protein and circular RNA is improved.

A method for designing a protein capable of binding in an RNA base selective manner or RNA base sequence specific manner is provided. The protein of the present invention is a protein containing one or more of PPR motifs (preferably 2 to 14 PPR motifs) each consisting of a polypeptide of 30- to 38-amino acid length represented by the formula 1 (wherein Helix A is a moiety of 12-amino acid length capable of forming an α-helix structure, and is represented by the formula 2, wherein, in the formula 2, A1 to A12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3, wherein, in the formula 3, the amino acids are numbered “i” (−1), “ii” (−2), and so on from the C-terminus side, provided that Liii to Lvii may not exist), and combination of three amino acids A1, A4 and Lii, or combination of two amino acids A4, and Lii is a combination corresponding to a target RNA base or base sequence.

The invention relates to a method for preparing a therapeutic RNA platelet carrier. The method comprises at least the following steps: transducing at least one therapeutic RNA sequence together with at least one therapeutic RNA packaging sequence comprising an RNA binding protein sequence to a megakaryocyte progenitor cell and / or a hematopoietic stem and progenitor cell expressing CD34, using a DNA-based vehicle; the present invention relates to a therapeutic RNA sequence and / or packaging sequence encoding at least one therapeutic RNA product in a megakaryocyte (e.g., HSPC), an immature megakaryocyte, and / or a megakaryocyte; activating expression of the therapeutic RNA sequence and / or the therapeutic RNA packaging sequence; and generating platelets from a mature megakaryocyte derived from a transduced progenitor cell of the megakaryocyte and / or a transduced hematopoietic stem and progenitor cell (HSPC) expressing CD34 and / or a transduced immature megakaryocyte and / or a transduced megakaryocyte, wherein the expression activation step is regulated to occur during megakaryocyte maturation and / or platelet formation wherein the generated platelet carrier is functionally reactive to activation with a specific agonist wherein the generated platelet carrier is activated by an extracellular signal, and wherein the expression activation step is regulated to occur during megakaryocyte maturation and / or platelet formation. And wherein the platelet carrier produced contains the at least one therapeutic RNA product. The invention also relates to a therapeutic RNA platelet carrier engineered by the above method and its therapeutic use. In addition, the present invention relates to a pharmaceutical composition comprising an RNA platelet carrier engineered by the above method and therapeutic uses thereof.

The present application relates to the field of physiology and molecular biology, and discloses an m 6 The present application relates to the field of physiology and molecular biology, and discloses an m 6 A binding protein IGF2BP3 ubiquitination and its application in preparation of an anti-tumor drug targeting RNA binding protein. Protein spectrum technology is used to screen the ubiquitination site of IGF2BP3, and the site mutation verifies that the ubiquitination site of IGF2BP3 is K213, which is located in the first KH domain of IGF2BP3. The functional analysis results show that after the mutation of IGF2BP3, the binding of IGF2BP3 with downstream tumor-related genes is weakened, the expression of the downstream tumor-related genes is down-regulated, and the growth of cervical cancer cells is inhibited, which indicates that ubiquitination modification is an important regulation mode affecting the function of IGF2BP3.

Described herein is a nucleic acid comprising a sequence encoding an epigenetic effector fusion comprising at least two epigenetic effectors. Described herein is an epigenetic editing system comprising any nucleic acid described herein and a nucleic acid encoding a gRNA comprising an RNA aptamer sequence that binds to the RNA binding protein. Described herein is a method of regulating gene expression, the method comprising introducing into a cell: any of the epigenetic modulation system described herein.

The invention discloses a nanoTn5-mediated RBP protein binding RNA (Ribonucleic Acid) detection method based on a nano antibody, supports in-situ multiplexing, and relates to the field of molecular biology and high-throughput sequencing. The method comprises the following steps: fixing tissues by using a cross-linking agent, and introducing a 5 '-Adapter-Nx-3' primer containing a random region to carry out in-situ reverse transcription so as to form an RNA / cDNA hybrid; adding species-specific RBP protein primary antibodies (such as rabbit antibodies and mouse antibodies), and combining target RNA binding proteins; then matching nano Tn5 which is resistant to primary antibody species specificity, and accessing the nano Tn5 into a pre-installed channel-containing label bar code Adapter-2; triggering in-situ transposition through divalent metal ions, so that Adapter-2 is inserted into the tail end of the hybrid; finally, a universal PCR primer is used for amplification and library building, and multiplexing omics data are obtained according to channel tag de-mixing. The invention supports single cell level detection and single / double channel parallel detection.

The present application provides a system and method for live cell RNA imaging and sensing. The system of the present application comprises: (i) a target recognition module comprising a circular binding RNA, the circular binding RNA comprising at least one target binding sequence configured to form a double-stranded binding region by complementary binding with a sequence on a target RNA; and (ii) a signal module comprising a double-stranded RNA binding protein and a signal element, the double-stranded RNA binding protein being connected to the signal element, wherein the double-stranded RNA binding protein recognizes and binds to the double-stranded binding region. The method of the present application comprises introducing the system into a live cell and performing imaging and detection. The system of the present application has the advantages of non-invasiveness, low fluorescence background and universality.

The invention discloses an RNA co-immunoprecipitation kit for specific binding of prion protein in muscle cells and an RNA extraction method, and relates to the technical field of bioengineering. According to the present invention, the specific co-precipitation kit preparation and the specific extraction steps comprise cell lysis, cell lysis solution-antibody-magnetic bead incubation, protein digestion and RNA extraction, such that the high purity and the sufficient amount of the enriched RNA are successfully ensured so as to completely meet the strict requirements of the subsequent RNA-seq sequencing. The method overcomes the inherent defects of the existing RIP technology in the research of non-classical RNA binding proteins, realizes the optimization of the whole process from high-specificity enrichment to high-quality sequencing sample preparation through the integrated innovation of methodology and the kit, has the outstanding advantages of strong specificity, high sensitivity, good repeatability, simple operation and the like, and has a wide application prospect in the research of non-classical RNA binding proteins. And remarkable technical progress is achieved, and a positive application effect is generated.

The invention discloses a method for synergistically improving the loading capacity of target nucleic acid in exosomes by utilizing electrical stimulation regulation and interaction with protein-RNA (Ribonucleic Acid) and application. Aiming at the problem that the existing exosome nucleic acid loading efficiency is low, the invention constructs a delivery system comprising RNA binding protein SYNCRIP, an exosome sorting sequence hEXO recognized by the RNA binding protein SYNCRIP, target nucleic acid (miRNA or shRNA) containing the hEXO sequence, a nucleic acid expression construct and an electrical stimulation induction module. The SYNCRIP is induced to be enriched in the exosome through electrical stimulation, and active and efficient loading of target nucleic acid is achieved through specific binding of the SYNCRIP and hEXO. The method has the advantages of high efficiency, universality, flexibility and simplified engineering steps, and has a wide application prospect in the field of nucleic acid drug delivery.

The present disclosure provides methods for simultaneously identifying dynamic and disease-associated RNA binding protein (RBP)-RNA interaction (PRI) sites at single nucleotide resolution across the entire transcriptome. The methods disclosed herein recapitulates PRI profiles obtained with several distinct conventional PRI methods in a single assay at efficiencies that are improved by orders of magnitude, and permit the identification of the specific RBP bound at a PRI.

The invention relates to an RNA (Ribonucleic Acid) co-immunoprecipitation-based RNA binding protein aggregate molecular function detection method, which comprises the following steps: S1) RNA co-immunoprecipitation: firstly, splitting tissues or cells, then cleaning by using magnetic beads to remove a splitting solution, and then preparing a detection sample; s2) protein and RNA detection: firstly carrying out semi-denaturation gel electrophoresis on the sample, confirming the IP efficiency of the sample, and then recovering RNA on the membrane; s3) releasing RNA from the membrane: incubating by adopting a prepared PK buffer solution to perform protein digestion so as to extract RNA, measuring the concentration of RNA, and performing reverse transcription to obtain RNA formed by combining a DAZL polymer and a DAZL monomer; s4) performing qPCR (quantitative polymerase chain reaction) detection on a target target: performing function detection, and verifying whether RNA (ribonucleic acid) exists in the aggregate formed by combining the DAZL polymer and the monomer. The method is simple, efficient and accurate, and provides a more convenient platform for functional research of the polyamyloid protein.

The present application relates to a fusion protein, in particular to a tumor microenvironment responsive fusion protein-siRNA complex prodrug system and application thereof. The carrier is a fusion protein coupled by PSTAG shielding sequence, tumor microenvironment enzyme responsive sequence, RNA binding protein sequence and human heavy chain ferritin. The carrier can bind and deliver siRNA drugs into cells to play a gene silencing effect.

The invention discloses application of polypeptide for inhibiting expression of inflammasome NLRP3 in preparation of pneumonia treatment drugs, and belongs to the technical field of biological medicines. Derived peptide is obtained based on a DTX4 protein functional domain, the peptide fragment is derived from an interaction region of DTX4 and RNA binding protein HuR, and the action mechanism of the peptide fragment is competitive binding with the HuR, so that the stabilizing effect of the HuR on mRNA of various inflammatory factors is blocked, the mRNA is promoted to be degraded, and expression and secretion of the inflammatory factors are inhibited from the level after transcription. The polypeptide disclosed by the invention has the potential of being developed into a novel anti-infectious pneumonia treatment medicine, and a brand new strategy is provided for treating bacterial infectious pneumonia.