56 results about "Polyadenylation" patented technology

The invention discloses a variable polyadenylation dynamic analysis method and device. The method comprises the following steps: acquiring initial space transcriptome data and an initial space bright field image; performing first preprocessing on the initial space transcriptome data to obtain target space transcriptome data; performing second preprocessing on the initial space bright field image to obtain a target space bright field image; performing data analysis and integration processing to obtain spatial variable polyadenylation data, spatial gene expression data and spatial cell distribution dynamic data; constructing a gene expression regulation network; generating an integrated analysis result; performing space-time analysis to obtain a space-time analysis result; performing trajectory analysis to obtain a trajectory analysis result; performing disease process analysis to obtain a disease process analysis result; and generating a variable poly-adenosine acidification dynamic analysis result. According to the invention, dynamic analysis of variable polyadenylation is realized, the accuracy is improved, and multi-angle biological understanding is provided. The method can be applied to the technical field of gene analysis.

The present invention relates to a method for assessing an autism spectrum disorder (ASD) in a sample from a subject, the method comprising (a) determining a parameter of alternative polyadenylation (APA parameter) in said sample; (b) comparing the APA parameter determined in step (a) to a reference, and (c) based on the comparison in step (b), assessing said ASD. The present invention also relates to polynucleotides, means for determining an APA parameter for use in diagnosis, databases, devices, and further methods related thereto.

The invention relates to a rep plasmid comprising at least one adeno-associated virus replication protein coding sequence encoding at least one functional rep protein, at least one polyadenylation signal sequence downstream the adeno-associated virus replication protein coding sequence, and a minimal element comprising one or more rep-binding elements downstream the polyadenylation signal sequence. In another aspect, the invention provides a transgene plasmid comprising a CMVie promotor, a transgene, SV40 PolyA, a 5' and a 3' inverted terminal repeats derived from J01901.1 AAV2; wherein the transgene plasmid is selected from one of the following: a conventional single-stranded genome recombinant adeno-associated virus, or a self-complementary genome recombinant adeno-associated virus.

The present application describes a coding nucleic acid sequence, particularly a messenger RNA (mRNA), comprising or coding for a histone stem-loop and a poly(A) sequence or a polyadenylation signal and the use thereof for increasing the expression of an encoded protein. It also discloses its use for the preparation of a pharmaceutical composition, especially a vaccine e.g. for the use in the treatment of tumours and cancer diseases, cardiovascular diseases, infectious diseases, autoimmune diseases or genetic diseases, or in gene therapy. The present invention further describes an in vitro transcription method, in vitro methods for increasing the expression of a protein using the nucleic acid comprising or coding for a histone stem-loop and a poly(A) sequence or a polyadenylation signal and an ex vivo and in vivo method.

The invention discloses a polyadenylation signal mutation harmfulness prediction method fusing an improved TabPFN network and SHAP interpretability. The polyadenylation signal mutation harmfulness prediction method comprises the following steps: 1, collecting a human polyadenylation signal mutation sample and carrying out pretreatment; 2, carrying out feature annotation on the mutation sample by using a computational biological tool; 3, selecting features by using a feature selection framework; 4, constructing a mutation prediction model based on the improved TabPFN; and 5, quantifying the contribution degree of each feature to a model prediction result by using an SHAP interpretability analysis technology so as to understand the output of a complex model and realize the interpretability of the model. The method provided by the invention solves the problems of complex parameter tuning, weak interpretability and the like in the prior art, so that the harmfulness of polyadenylation signal mutation is accurately, efficiently and interpretably predicted.

Disclosed are in vitro transcribed (IVT) messenger RNAs (mRNAs) comprising a polynucleotide that encodes human TJP2 gene, a 5' terminal cap, and a poly-adenylation (poly- A) tail at the 3' terminal end. In aspects, the polynucleotide is substantially free of uridine bases and comprises pseudouridine bases. Methods, compositions and uses employing the IVT mRNA for treating or preventing progressive familial intrahepatic Cholestasis type IV (PFIC type 4) in a patient in need thereof is also disclosed.

The present invention relates to an isolated nucleic acid comprising a nucleotide sequence encoding a mutated HPPD protein, wherein said mutated HPPD protein has HPPD activity, wherein in said mutated HPPD protein at least one amino acid has been replaced so that the resulting amino acid sequence comprises at least one amino acid selected from certain amino acids at specific positions important for conferring an increased HPPD inhibitor tolerance. The present invention also relates to proteins encoded by the nucleic acid of the invention, to chimeric genes, plant cells comprising the nucleic acid of the invention operably linked to a plant-expressible promoter and optionally a transcription termination and polyadenylation region, plants essentially consisting of the plant cells of the invention and methods of obtaining transgenic plants.

The application discloses a method and device for identifying a selective polyadenylation cell subpopulation, an equipment and a readable storage medium, and relates to the technical field of cell subpopulation identification. The method comprises the following steps: obtaining a selective polyadenylation expression count matrix containing a plurality of spots in spatial transcriptome data, spatial coordinate information of each spot, and a phenotype label of each spot; constructing a spatial adjacency graph of each spot based on the spatial coordinate information; training a graph attention network model by taking the selective polyadenylation expression count matrix and the spatial adjacency graph as input and taking the phenotype label as a supervision signal until the graph attention network model converges; predicting the confidence of each spot based on the graph attention network model; and taking each spot with a confidence higher than a preset confidence threshold as the selective polyadenylation cell subpopulation. The method increases the identification accuracy of the selective polyadenylation cell subpopulation.

To provide adeno-associated variants, formulations and methods for pulmonary delivery.SOLUTION: The present disclosure provides variant AAV capsid proteins that confer tropism for lung cells, as well as recombinant adeno-associated viruses comprising the variant AAVs and pharmaceutical compositions comprising the same, and their use in the delivery of heterologous nucleic acids to lung cells for the treatment of lung disorders. (ii) nucleic acids comprising, from 5 ' to 3 ', (a) AAV2 terminal repeats, (b) a promoter, (c) a nucleotide sequence encoding a human cystic fibrosis transmembrane conductance regulator (CFTR) or a biologically active truncated CFTR lacking amino acids 708 to 759 of the human CFTR sequence, (d) a poly-adenylation sequence, and (e) AAV2 terminal repeats.SELECTED DRAWING: None

Disclosed herein are gene therapy vectors used for efficiently transducing cells to express a human β-globin gene. Specifically disclosed is an expression vector which comprises: an expression cassette for a β-globin gene, which comprises exons and introns of human β-globin gene, as well as cis-acting elements including one or more of WPRE, SV40 polyadenylation signal and / or SV40 ori. The disclosed expression vectors have significantly enhanced viral vector packaging efficiency in viral vector packaging cell lines, which leads to effective integration of lentiviral vectors and high expression level of β-globin gene in target cells. Also disclosed are pharmaceutical compositions and therapeutic methods utilizing such expression vectors.

This invention relates to an improved recombinant polyadenylated signal sequence and its use.

The invention provides polynucleotide constructs for the regulation of gene expression by aptamer-based modulation of U1 small nuclear ribonucleoprotein (snRNP)-mediated suppression of polyadenylation and methods of using the constructs to regulate gene expression in response to the presence or absence of a ligand that binds the aptamer. The polynucleotide construct contains a U1 binding site in the context of a riboswitch comprising an effector region and an aptamer such that when the aptamer binds a ligand, target gene expression occurs.

A vector for use in treating cognitive decline and / or memory deficits in a subject in need thereof includes an expression cassette that includes a nucleic acid encoding asprosin and / or an analogue thereof, operably linked to one or more regulatory elements that promote expression of the asprosin and / or an analogue thereof coding sequence, wherein the one or more regulatory elements include a nucleic acid promoter, a polyadenylation (poly(A)) tail signal, and / or posttranscriptional regulatory element.

The present invention describes that a pre-mRNA molecule, which temporarily exists before polyadenylation-site induced cleavage occurs, can be targeted by RNase H recruiting antisense oligonucleotides downstream of a transcripts 3' terminus to reduce expression levels of target genes from which the RNA polymerization originates.

The invention provides a spatial complete transcription sequencing method suitable for tobacco petiole tissues and application. According to the method, a tissue embedding method and a freezing slicing method suitable for the tobacco petioles are adopted, it is effectively guaranteed that tobacco petiole slices are uniform and flat, and the structure is kept complete; the pretreatment liquid suitable for being used before plant tissue permeabilization is adopted, plant tissue cell walls can be effectively subjected to enzymolysis, cell membrane permeability can be improved, and RNA can be better released; a treatment method suitable for in-situ polyadenylation of tobacco petiole tissues is adopted, so that in-situ polyadenylation can be effectively performed on non-coding RNA in a slice sample, and the capture efficiency of the non-coding RNA is improved; by adopting the method which is suitable for a space whole transcriptome sequencing process and can remove the rRNA from the cDNA library, the rRNA can be effectively removed from the library through a wet experiment end, the situation that the sequencing depth of other RNA types is reduced due to the fact that the amount of captured ribosome RNA is too high is avoided, and the data utilization rate is greatly increased. The method has a wide application prospect.

The present invention provides an AP plasmid, characterized in that the plasmid expresses the gIII-neg protein and has one or more RyhB binding sequences shown in SEQ ID No. 1 inserted into the rear of its ribosome binding site. Also disclosed are its application in the PACE directed evolution of the PAP I enzyme and a PACE directed evolution system for the PAP I enzyme. Also disclosed are screened PAP I enzyme mutants, encoding genes, prokaryotic expression vectors, and prokaryotic expression systems. The present invention introduces Escherichia coli non-coding RNA RyhB sRNA into the PACE directed evolution method to inhibit the translation of the gIII-neg protein and eliminate the adverse effects of the gIII-neg protein on the packaging of progeny phages. The stronger the polyadenylation activity of the PAP I, the longer the half-life of RyhB can be extended, promoting the latter's translational inhibition of the gIII-neg protein. After multiple passages, the phage forms a population advantage and is isolated and sequenced, ultimately obtaining a PAP I with significantly improved activity.

The invention discloses a gene expression enhancing element capable of improving a gene transcription level and an application of the gene expression enhancing element. It is found that a delta satellite region from sweet potato mosaic virus (SPLCV) SBG51 comprises a new DNA sequence capable of remarkably enhancing expression of a reporter gene, the gene expression enhancing effect of the delta satellite region does not change polyadenylation of mRNA, the delta satellite region is independent of a promoter and a terminator, and the space-time mode of the promoter is kept. The invention further finds that AT-rich sequences (such as ATAAA or TTAAA or tandem repeat sequences containing a plurality of ATAAA or TTAAA) are key elements of the above effects, even synthetic AT-rich sequences (AT-rich-1 and AT-rich-2) of 29bp are sufficient to increase the expression of the reporter gene GFP by about 3 times, and the gene expression enhancement effect of the AT-rich sequences is well expressed in both plants and yeast cells. Therefore, the invention can be applied to the aspects of improving the activity of the target gene according to the required level, providing high-level and long-lasting protein production and the like.

The invention relates to a rep plasmid comprising at least one adeno-associated virus replication protein coding sequence encoding at least one functional rep protein, at least one polyadenylation signal sequence downstream the adeno-associated virus replication protein coding sequence, and a minimal element comprising one or more rep-binding elements downstream the polyadenylation signal sequence In another aspect, the invention provides a transgene plasmid comprising a CMVie promotor, a transgene, SV40 Poly A, a 5' and a 3' inverted terminal repeats derived from J01901.1 AAV2; wherein the transgene plasmid is selected from one of the following: a conventional single-stranded genome recombinant adeno-associated virus, or a self-complementary genome recombinant adeno-associated virus.

A transposon is provided comprising a nucleic acid sequence traversing the chromatin open element (UCOE) as well as a nucleic acid sequence of a gene of interest or a fragment thereof under the control of a promoter and optionally a 3'polyadenylation sequence, both sides of which are Piggybactransposon-specific inverted terminal repeats PB 5 'ITR and PB 3' ITR.

The present invention is directed to polynucleotides, and to vectors comprising the polynucleotides, that are useful for the expression of a CTNNB1 transgene in cells and for use in gene therapy of CTNNB1-related disorders. In one aspect of the invention there is provided a nucleic acid construct comprising: a promoter operably linked to a nucleotide sequence encoding a functional CTNNB1 polypeptide; a 5' untranslated region (UTR) of a human CTNNB1 gene or a fragment of said 5' UTR; a microRNA (miRNA) targeting region; and a polyadenylation signal.

The present disclosure provides a Her2 antibody that can be expressed with an adeno-associated virus. The present disclosure provides a gene expression cassette comprising a coding sequence of an anti-Her2 antibody or an antigen binding fragment thereof, and at least one of a promoter, an intron and a polyadenylation signal, the anti-Her2 antibody or the antigen binding fragment thereof comprises a light chain variable region and a heavy chain; the light chain variable region comprises a sequence having at least 85% identity with SEQ ID NO: 2; the heavy chain has a sequence that is at least 85% identical to SEQ ID NO: 3 or 5. According to the present invention, the problems caused by the direct application of the antibody in the gene therapy in the prior art are avoided through the antibody structure modification, and the efficient transduction can be achieved when the antibody is used for the gene therapy through the antibody structure modification and the design of the gene expression box, the carrier and the like.

Disclosed is a recombinant adeno-associated virus (rAAV) vector that is a universal reference standard in quantitative PCR assays used to determine the genome copy titer of rAAV-transgene particles. The rAAV-Universal Standard vector includes multiple nucleotide sequences that are targets for PCR assays to support polymerization such as fragments of commonly used promoters, enhancers, polyadenylation sequences, and reporter genes found in rAAV constructs. Those multiple targets ensure that there is a positive reaction and thus provide a standard, positive control and calibrator to assure proper performance of the quantitative PCR assays without the need to use a separate reference standard for each particular rAAV particle assayed. The rAAV-Universal Standard is produced in multiple AAV serotypes and may encode a functional reporter gene to further provide a universal positive control for analytical assays of rAAV-transgene particles.

Provided herein are methods and materials for performing pooled screening, modulating RNA processing events, and / or analyzing a sample to identify an RNA processing event or RNA processing target associated with a condition. For example, an RNA processing event can be alternative splicing, constitutive splicing, polyadenylation, methylation, folding, degradation, pseudouridylation, and / or adenosine to inosine RNA editing. In some embodiments, the method includes selecting for a phenotype of interest.

The invention discloses a plasmid vector for stable expression of mammalian cells as well as a construction method and application of the plasmid vector, relates to the technical field of genetic engineering, and discloses a plasmid vector for stable expression of mammalian cells. The plasmid vector comprises a promoter, a polyadenylation signal, an internal ribosome entry site IRES, a replication start site, a selection marker gene and a specific gene; according to the plasmid vector for stable expression of the mammalian cells as well as the construction method and the application of the plasmid vector, an EBNA1 / oriP system is constructed, EBNA1 protein can be specifically combined with an oriP sequence on the plasmid, and the plasmid is firmly adhered to a host cell genome like an anchor and is prevented from being discharged or lost by the cells, so that a target gene can be stably inherited and expressed for a long time along with cell division, and the expression efficiency is improved. The problem of plasmid loss is solved from the source; and the plasmid vector can drive a target gene in various mammalian cells to realize efficient and stable expression of a cross-cell line, and is extremely high in universality.

Provided herein is an expression cassette, the expression cassette comprising: 1) a chimeric promoter, the chimeric promoter comprising an hTERT promoter and a minimum promoter; 2) a coding sequence (CDS); and 3) a poly (A) sequence or a polyadenylation signal sequence. The CDS sequence in the expression cassette is only expressed in a tumor or a cancer cell, or the expression level in the tumor or the cancer cell is far higher than the expression level in a normal cell, so that the expression cassette can be used for treating cancer.

The embodiment of the invention provides a method and system for analyzing spatial transcriptome data, and belongs to the technical field of data analysis. The system comprises a data uploading and quality control module which is used for uploading spatial transcriptome data, bright field pictures and sample clinical information and performing quality control on the uploaded data; the spatial multi-omics feature identification and integration module is used for identifying spatial multi-omics features, integrating multi-omics data, carrying out batch processing on the data and unifying a data format; the spatial multi-omics data analysis module is used for performing data analysis of gene expression, genome variation, RNA modification, variable polyadenylation and pathogen and cell distribution dynamics according to different omics data types; the user management module is used for providing multi-level authority management; and the analysis report module is used for automatically generating analysis report data. According to the method, the depth and breadth of spatial transcriptome data analysis can be improved, and spatial multi-omics features can be analyzed more comprehensively and accurately.

The invention discloses a gene combination for detecting Alzheimer's disease and application of the gene combination. The gene combination comprises any one or at least two of the following combinations: (1) a gene combination based on mRNA expression change; (2) gene combination based on variable shear change; and (3) a gene combination based on variable polyadenylation change. According to the invention, mRNA (messenger ribonucleic acid) is expressed, and altered splicing is carried out; the invention relates to a method for preparing a polyadenylation system, which comprises the following steps of: preparing a polyadenylation system (AS, AS) and a polyadenylation system (altered polyadenylation; according to the method, three transcriptional regulation and control layers (APA, APA) are subjected to conjoint analysis, so that the understanding of AD pathogenesis is increased, a part of problems related to the AD pathogenesis are answered, the influence of different risk genes on AD can be deeply understood, the auxiliary diagnosis of AD is realized, and a possible disease prevention or treatment method is determined.

A partially or fully differentiated iPSC-derived microglia cell comprising a transposon comprising a Ubiquitous Chromatin Opening Element (UCOE) nucleic acid sequence, and a nucleic acid sequence of a gene of interest or a fragment thereof and optionally a 3' polyadenylation sequence under control of a promoter, flanked by transposon-specific inverted terminal repeat sequences 5' ITR and 3' ITR.

The invention discloses a single cell 3'end transcriptome variable polyadenylation (APA) analysis method, and belongs to the field of bioinformatics. The analysis process provided by the invention is based on 3'end transcriptome sequencing data of a single cell, combines multiple processes of UMI deduplication, false comparison removal, site merging, internal amplification removal, polyA site removal with few supporting cells, site verification and the like, and can realize efficient detection and quantification of APA at the single cell level. The method is especially suitable for single cell APA analysis of single cell 3'end transcriptome sequencing data, including 3 'end single cell sequencing data after 10x scRNA-Seq cell subset combination, 3' end single cell sequencing data based on a C1 chip, and even full-length transcriptome data.

The invention provides chemically-modified adenosine triphosphate and a preparation method and application thereof.The chemically-modified adenosine and the chemically-modified adenosine triphosphate are synthesized by means of chemical synthesis, natural adenosine in mRNA is globally replaced with the chemically-modified adenosine, and the chemically-modified adenosine triphosphate is obtained. Or the mRNA is subjected to polyadenylation tailing modification, so that the translation efficiency and the stability of the target mRNA are enhanced, the immunogenicity is reduced, and a supplement and a new choice are provided for an mRNA modification technology.