71 results about "RNA-Binding Motif" patented technology

The present disclosure provides compositions and methods for the targeted modification of RNA molecules by RNA prime editing. The compositions and methods may be conducted invitro or in vivo within cells (e.g., human cells) for the therapeutic correction of disease-causing mutations and / or installation of motifs or mutations in RNA molecules of interest as a tool for scientific research. The disclosure provides compositions and methods for conducting RNA prime editing of a target RNA molecule (e.g., an RNA transcript) that enables the incorporation of one or more nucleotide changes and / or targeted mutagenesis of a target RNA molecule. The nucleotide change can include a single-nucleotide change, an insertion of one or more nucleotides, or a deletion of one or more nucleotides. More in particular, the disclosure provides a variety of configurations of the RNA prime editors each comprising a nucleic acid programmable RNA binding proteins (napRNAbp), such as Cas13, and an RNA-dependent RNA polymerase (RDRP), which are provided as fusion proteins or which can be separately provided in trans. The RNA prime editors are guided to a target RNA site by a guide RNA, which can be a rpegRNA that includes a template region for the synthesis of an RNA sequence to be installed on the RNA molecule attached to an available 3′ terminus. In others embodiments, the RNA template can be provided in trans.

The present disclosure relates to methods of identifying RNA targets of RNA binding proteins. In aspects, the disclosure relates to a method of identifying RNA molecules bound by RNA binding proteins. Some embodiments of the present disclosure relate to a method that can definitively identify direct RNA-target interactions with targeted proteins without the requirement for immunoprecipitation or gel extraction. In some embodiments, the method may include combining multiple antibodies in the same sample.

The invention discloses an RNA (Ribonucleic Acid) binding protein enrichment analysis method based on single cell expression profile data, which comprises the following steps of: writing an interactive online Web application program by using Shiny, carrying a data visualization tool, and using an RBP (Reactive Binding Protein)-gene database as a database; the method is specially designed for single cell data, different single cell data can be integrated for enrichment analysis, and expression profiles and RBP dynamic changes in single cells can be effectively captured and analyzed; rBP enrichment analysis is customized for single cell data, a single group and multiple groups of single cell expression data are preprocessed, including normalization processing, and a statistical model is used to evaluate enrichment significance at each time point, so that the analysis accuracy and biological correlation are improved; a dynamic visualization tool is provided, the dynamic visualization tool comprises a customizable network diagram, an interactive bar diagram and detailed table display, and a user can adjust a plurality of parameters of a view according to needs and directly download images and data from an interface.

The present invention provides novel RNA base editing compositions, systems, methods and uses. Guide RNAs for site-specific RNA editing of RNA encoding transcriptional coactivators YAP1 or TAZ are provided, and compositions and systems comprising the same with a programmable RNA binding protein (e.g. a Cas protein) and / or a base editor. Methods for RNA editing of YAP1 or TAZ are also provided. RNA editing of YAP1 or TAZ is used for targeting phosphorylation sites, and activating transcription of proteins in regenerative therapy for treating cardiac disease.

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.

The invention discloses a targeted enrichment method for proteome. According to the cell nucleus targeted RNA binding protein enrichment reagent, one end is provided with a furocoumarin group, the other end is provided with a cell nucleus targeted group, and the other end is provided with biotin; the enrichment or identification of the RNA binding protein in the cell nucleus can be carried out. The method for enriching the nucleus-targeted RNPs by adopting the nucleus-targeted RNA binding protein enrichment reagent comprises the following steps: firstly, adding the nucleus-targeted RNA binding protein enrichment reagent into cells for co-incubation, then, irradiating a cell incubation system by adopting ultraviolet light with the wavelength of 254nm, and then, irradiating the cell incubation system by adopting ultraviolet light with the wavelength of 365nm, then carrying out cracking to obtain a cracking solution; incubating the lysis solution and streptavidin magnetic beads, and finally collecting the magnetic beads enriched with the cell nucleus RNPs, so that the cell nucleus targeted RNPs are enriched. According to the method, the cell nucleus positioning of the reagent can be efficiently realized, the RBPs enrichment selectivity and the negative electrode efficiency are improved, and the varieties of RNPs obtained through enrichment are more comprehensive.

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 peanut protein content related molecular marker and related application. The molecular marker is located at 95485614bp-95490150bp of peanut chromosome 1, is an RNA binding protein KH domain-containing protein gene, and a SNP site (T / A) is detected at 95487145bp, namely, the gene is on the complementary strand, the position (CDS sequence 1229th base) on the gene sequence is A in the low-protein peanut group and T in the high-protein peanut group, and a mutation from lysine to isoleucine (protein 410th amino acid) is caused. The application provides a new marker for peanut high-protein resource molecular marker assisted selection for the first time, and has very important significance for high-protein peanut resource screening and high-protein peanut new variety breeding.

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.

The invention belongs to the field of biological medicine, and particularly discloses a pharmaceutical application of an AR agonist based on bioinformatics targeted screening in sepsis sarcopenia, and the core is that the AR agonist Ostarine is adopted to specifically activate muscle AR and improve SIS through subcutaneous injection administration in the acute stage (within 5 days) of sepsis. The mechanism comprises the following steps: (1) recovering skeletal muscle protein synthesis (up-regulating p-AKT / p-mTOR) and decomposing metabolic balance (down-regulating Atrogin-1 / MuRF1); (2) promoting the expression of a polyamine biosynthetic gene (AMD / ODC1 / SMOX); and (3) adjusting the ratio of fast and slow muscle fibers (promoting MyoD and inhibiting MHC I and TnI-flow). Experiments show that Ostarine (5mg / kg) can significantly improve the survival rate, muscle weight and grip strength of sepsis mice within 5 days and reverse amyotrophy. In addition, the invention provides an SIS drug screening method based on the RNA binding protein Hnrnpa1 (regulating AR pre-mRNA). The method is easy and convenient to operate and high in targeting performance, and a new strategy is provided for treatment of sepsis sarcopenia.

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 RNA (Ribonucleic Acid) binding protein HuR and a gene of the RNA binding protein HuR as a target spot in screening of a medicine for treating senile deafness, belongs to the technical field of genetic engineering, and provides application of the RNA binding protein HuR gene as a therapeutic target spot in screening of a medicine for preventing or treating senile deafness. The RNA binding protein HuR is used as a therapeutic target to screen the medicine for preventing or treating the senile deafness. According to the application disclosed by the invention, the HuR is knocked out from the inner ear hair cells and the whole cochlea of the mouse by utilizing Atoh1-Cre and Pax2-Cre mice respectively, and the condition that the degeneration of static cilia is caused by the deletion of the HuR in the hair cells is found, so that the hair cell senescence is accelerated, and the premature hearing loss is further caused. The results show that the HuR plays an important role in maintaining a static cilia steady state, delaying hair cell senescence and preventing senile deafness, and provides a therapeutic target for clinically preventing and improving hearing loss of senile deafness patients.

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 invention provides an improved method for identifying interaction between RNA and RNA binding protein, and relates to the field of biological analysis. Comprising the following steps: ultraviolet crosslinking: carrying out covalent crosslinking on RNA and binding protein in cells through ultraviolet rays, and fixing instantaneous transition of interaction between RNA and RNA binding protein; s2, cell lysis and fragmentation: splitting the cells treated in the step S1, and then cutting RNA into short fragments by using RNA enzyme; s3, immunoprecipitation: enriching the target RBP and the RNA fragment combined with the target RBP by using a specific antibody; s4, linker connection and library construction: firstly, carrying out reverse transcription on RNA molecules by using a random primer to form a cDNA first chain; then synthesizing a cDNA second chain by using dNTP (deoxyribonucleoside triphosphate) containing dUTP (deoxyuridine triphosphate) and DNA polymerase; carrying out terminal repair and A addition on the double-stranded DNA; connecting a double-chain DNA (deoxyribonucleic acid) joint with a protruding T basic group at the tail end; carrying out PCR amplification to obtain a sequencing library; and S5, performing high-throughput sequencing. The treatment of FastAP and PNK is omitted, the loss of RNA molecules is reduced, and the experimental period is shortened.

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.