50 results about "RNA modification" patented technology

The invention discloses a method for predicting an RNA (Ribonucleic Acid) methylation site, which is based on a multi-modal feature fusion and semantic vector embedding technology and is used for remarkably improving the recognition precision of an m7G modification site. The method comprises the following steps: firstly, constructing an RNA sequence data set containing positive and negative samples, and dividing the RNA sequence data set into a training set and an independent test set according to a predetermined proportion; then, multi-modal features are extracted through One-hot coding (One-hot), nucleotide chemical property coding (NCP), electron-ion interaction potential coding (EIIP) and local nucleotide composition coding (ENAC), and context semantic information of a nucleotide sequence is obtained in combination with a DNA2Vec model; according to the model, a multi-modal feature fusion path (MRF) and a DNA2Vec embedding path are adopted, after feature dimension compression is carried out through a full connection layer, a Transform encoder is used for capturing a long-range dependency relationship, and a prediction probability is calculated through a Sigmoid activation function. In the optimization process, batch normalization, Dropout and Adam optimizers are adopted, and the binary cross entropy loss function is minimized. Finally, the performance of the model is evaluated through five-fold cross validation, and the generalization ability of the model is verified on an independent test set. According to the method, through multi-source feature fusion and hierarchical modeling, the analysis capability of sequence information is remarkably improved, and an accurate calculation tool is provided for RNA modification prediction.

Aspects of the present disclosure are directed to at least methods and compositions for diagnosis and / or treatment of diseases associated with aberrant levels of m5C RNA, including but not limited chromatin associate RNA (caRNA). The disease may comprise cancer and / or pre-cancerous cells. The disease may be associated with mutations in a TET2 pathway, including but not limited to mutations in TET2, IDH1, IDH2, and / or ASXL1 encoding genes. Treatment of a disease may comprises administration of one or more inhibitors of MBD6, TET2, and / or NSUN2. Also provided herein are methods of treatment of a disease in an individual comprising administering one or more inhibitors of MBD6, TET2, and / or NSUN2 to the individual determined to have aberrant m5C RNA modifications.

The invention belongs to the technical field of biological medicine, and particularly relates to a reagent for detecting glycosylation modified RNA and application of the reagent in lung cancer metastasis prediction. According to the invention, glycosylation modification after RNA transcription is associated with the important pathological process of lung cancer metastasis for the first time, and a new theoretical basis and target are provided for diagnosis and treatment of lung cancer metastasis. In the prior art, the expression levels of genes and proteins are mainly concerned, and the invention goes deep into the RNA modification level and provides deeper and more accurate molecular information. And secondly, by detecting the glycosylation modification level of the LADENI, not only the expression quantity of the LADENI, the specificity and sensitivity of the LADENI as a biomarker are improved. The modification is dynamic and closely related to the function, so that the metastasis potential of the tumor cells can be reflected more accurately.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

This invention relates to a method for designing and utilizing a broad RNA modification library that includes all surrounding sequences of the RNA modification. By introducing multiple types of RNA modifications, this invention enables the construction of RNA modification libraries that encompass all possible combinations of surrounding sequences flanking the modified RNA. Therefore, it differs from existing reported methods for constructing RNA modification libraries. Furthermore, using the RNA modification library of this invention for single-molecule RNA sequencing generates a high-quality reference dataset containing all possible combinatorial motifs. If this dataset is used as training data for deep learning (or machine learning), it overcomes the limitations of existing software that is limited to specific RNA modifications or has low prediction accuracy for other modifications. This allows for the development of novel, more accurate RNA modification detection software and the simultaneous detection of multiple RNA modifications.

Aspects of the present disclosure are directed to at least methods and compositions for diagnosis and / or treatment of diseases associated with aberrant levels of m5C RNA, including but not limited chromatin associate RNA (caRNA). The disease may comprise cancer and / or pre-cancerous cells. The disease may be associated with mutations in a TET2 pathway, including but not limited to mutations in TET2, IDH1, IDH2, and / or ASXL1 encoding genes. Treatment of a disease may comprises administration of one or more inhibitors of MBD6, TET2, and / or NSUN2. Also provided herein are methods of treatment of a disease in an individual comprising administering one or more inhibitors of MBD6, TET2, and / or NSUN2 to the individual determined to have aberrant m5C RNA modifications.

The invention belongs to the technical field of RNA modification detection, and particularly relates to a method for distinguishing four terminal small RNAs through APB small RNA imprinting hybridization. RNA to be detected is subjected to phosphatase and T4 polynucleotide kinase treatment, RNA purification and APB small RNA imprinting hybridization, the response condition of the RNA to phosphatase and T4 polynucleotide kinase is obtained by comparing whether the electrophoresis migration rate before and after treatment is changed or not, and then the terminal types of 2 ', 3' OH, 2 'OMe, 2', 3'cP and 3 'P before treatment are deduced. Compared with a traditional small RNA imprinting hybridization method, the method has the advantages that the migration rate difference of bands of different modified small RNAs during APB gel electrophoresis is larger, and the problems that the migration rate difference of different modified RNAs is small, and experimental results are often difficult to judge due to the influence of RNA purity, concentration and experimental conditions in a traditional method are solved; the method has a good application prospect in the fields of small RNA modification and functional research thereof.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and / or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

In various aspects, the invention provides a method of detecting nucleotide modifications in a sample comprising RNA, the method comprising reacting RNA in the sample with periodate to form periodate-treated RNA in the sample, sequencing the periodate-treated RNA in the sample, and detecting a modification signature in the sequence.

The disclosure relates to nucleic acid engineering and, more specifically, to synthetic RNA constructs and assembly methods that enable precise, site-specific inclusion of one or more RNA base modifications in a controlled and extendable sequence context suitable for long-read sequencing and quantitative benchmarking. Disclosed are methods of making a modular RNA construct. The methods may comprise annealing a modification loop bait RNA oligonucleotide with a hairpin RNA oligonucleotide, a modification loop RNA oligonucleotide, and a poly-A splint RNA oligonucleotide; and ligating the annealed oligonucleotides to form the modular RNA construct.

The present invention relates to a method classifying target RNA modifications in a neural network system, to a method for training a neural network system that is configured to classify target RNA modifications, to a neural network system, to a computer system adapted to classify target RNA modifications, to a computer program and to a non-transitory readable medium.

The present disclosure provides, for instance, a method of detecting and quantifying RNA modifications. The RNA modification may be, for example, m6A, m6Am, m1A, hm5C, m5C, Ψ, or inosine. The method can comprise contacting the RNA with an antibody that binds the modification, and using a bar code approach to quantify the amount of RNA.

The present disclosure relates to the identification of a novel nucleoside modification, referred to herein as anhydride U, present in tRNA molecules within the cell. The present disclosure further relates to the enzymatic and chemical production of anhydride U as well as methods for detecting and regulating the presence of anhydride U within the cell.

Disclosed herein is a method for training a framework comprising one or more models for site-specific ribonucleic acid (RNA) modification detection on an RNA sequence of interest, comprising receiving a training dataset of sequences, each sequence being either an unmodified RNA sequence or a modified RNA sequence and, for each sequence, annotations indicating whether the respective sequence contains a modification at one or more sites; extracting a sequence context read j from each sequence, and extracting, for each site of interest i in read j, i being a site at which it is desired to detect a modification, a site-specific annotation from the annotations, the site-specific annotation indicating whether a specific modification m occurs at site i; training at least one said model to determine a probability of modification m at site i, using a plurality of k-mers, extracted from each read j, including one or more k-mers from before site i, at site i, and after site i; updating the at least one model based on a loss between the probability and the site-specific annotation; and outputting the framework, after a predefined number of epochs for training has been completed.

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of RNA modifications in cell-free RNA. The RNA modification can be used to generate an RNA modification signature in cell-free RNA from a patient.

The present invention discloses a method for highly sensitive quantitative detection of inosine in RNA, and belongs to the field of biotechnology. The method of the present invention comprises the following steps: enzymatically digesting a cell sample to be tested or an RNA sample to be tested into a single nucleoside; performing a derivatization reaction on the digested nucleoside using CMCT; performing dispersed solid phase extraction on the derivatized product using CeO2; and performing LC-MS / MS analysis on the extracted sample. CMCT can selectively react with the NH group at the N1 position of inosine to generate I-CMCT, which can greatly improve the detection sensitivity of LC-MS / MS; CeO2 can selectively enrich I-CMCT and remove compounds such as CMCT that do not contain cis-hydroxyl groups. The method of the present invention is simple and efficient, has a mild reaction, is easy to operate, and has high sensitivity. It has great potential in determining endogenous modifications of trace RNA and a small number of cells (as low as a single cell), and is helpful for functional studies of RNA modifications in precious biological samples.

The invention belongs to the technical field of RNA (Ribonucleic Acid) molecular event detection, and particularly discloses a method for screening a modification enzyme marker and detecting an RNA molecular event in a cell. The method comprises the following steps: screening RNA modification enzymes possibly used for RNA molecule event marking, marking RBP binding, translation and subcellular localization experienced by RNA molecules in cells by using the screened modification enzymes, and finally detecting the marker by using a high-throughput sequencing method. In the aspect of RBP binding event detection, the method does not depend on an antibody, is simpler to use, can be compatible with long read length sequencing and single cell sequencing, and is wider in application range. In the aspect of ribosome translation event detection, the method can be compatible with long-read-long sequencing, and the resolution of translation event analysis is improved. In the aspect of RNA subcellular localization detection, RNA components in membrane-free organelles which are difficult to separate can be marked; compared with other proximity labeling methods at present, the method has the advantages that the labeling efficiency is higher, the cell survival is not influenced by labeling, and the RNA positioning condition can be continuously monitored.

Provided are methods for using chimeric proteins to produce RNA modifications that can be detected by sequencing methods, including methods detecting relative translation rates of various mRNAs. Also provided herein are compositions comprising chimeric proteins, wherein the chimeric proteins comprise a RNA editing protein and a ribosomal protein.

The present invention relates to a method for designing a wide range of RNA modification libraries including all surrounding sequences of RNA modification and a use thereof. The present invention can construct a modified RNA library by introducing various types of RNA modifications and can reflect all possible combinations of surrounding sequences on both sides of the modified RNA library, thereby differing from the previously reported modified RNA library construction method. In addition, when single-molecule RNA sequencing is performed using a modified RNA library according to the present invention, a high-quality reference data set including all combinatorially possible motifs can be generated. Using this dataset as training data for deep learning (or machine learning) makes it possible not only to develop new RNA modification detection software with higher accuracy, but also to simultaneously detect multiple RNA modifications in a single analysis, beyond the limitations of existing software, which are often restricted within specific RNA modifications or exhibit reduced prediction accuracy for other modifications.

The present invention belongs to the field of biomolecular technology, and in particular to a kind of RNA-modified live cell imaging system and its composition and application. The RNA-modified live cell imaging system comprises an RNA reporter system and a FRET probe, wherein the RNA reporter system comprises a tetracycline-induced expression system, an mMaroon1 fluorescent protein, an NLS-nuclear localization sequence and a 22-repeat m6A-MS2 reporter sequence; the FRET imaging probe comprises a YTH domain, a YPet fluorescent protein, a long-chain flexible linker, an ECFP fluorescent protein, an MCP protein and an NLS nuclear localization signal. The m6A-modified live cell imaging system developed by this patent can perform high-resolution real-time dynamic imaging of m6A modification in living cells, and can realize triple dynamic monitoring of m6A modification levels and RNA localization and translation, thereby building a research platform and drug screening platform for m6A modification pathways.

The invention discloses a deoxyribozyme probe capable of specifically distinguishing a G-quadruplex and a single-strand structure of a G-rich sequence and application of the deoxyribozyme probe, and belongs to the technical field of deoxyribozyme probes. The method comprises the following steps: firstly, connecting a phosphorylated library enzyme chain with a substrate chain containing RNA (Ribonucleic Acid) modification sites to construct a linear DNA (Deoxyribose Nucleic Acid) library; then, under the condition that the pH is 7.4, co-incubating the library and a G-rich sequence in a single-chain state, separating and purifying a DNA strip for cutting an RNA site in the library, recovering a positive-sense strand after PCR amplification, and carrying out multiple rounds of screening to obtain the chain deoxyribozyme probe. The obtained probe can specifically detect a G-rich sequence in a single-chain form, has no response to a G-quadruplex structure, and has a good application prospect in the field of biosensing.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and / or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

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 provides a mutant tRNA (transfer ribonucleic acid) capable of specifically decoding a pseudouracil modified codon in a transcriptome and a translation group. In addition, the invention also provides a translation system containing the mutant tRNA, and a method for realizing site-specific amino acid insertion by responding to the pseudouracil modification codon based on the mutant tRNA. Furthermore, the invention also provides an RNA modification assisted codon expansion (RCE) technology based on the mutant tRNA.

The invention relates to a general library building method for trace RNA modification detection and application of the general library building method in RNA modification detection. The general library building method comprises the following steps: S1, collecting an RNA sample without ribosomal RNA; s2, repairing the tail end of the RNA sample; s3, taking the RNA chain in the S2 as a template, carrying out reverse transcription to form a first cDNA chain, synthesizing a second cDNA chain, and hydrolyzing the template; s4, taking the second cDNA as a template, and carrying out in-vitro transcription to obtain an RNA chain; s5, taking the RNA chain in the S4 as a template, and carrying out reverse transcription to obtain a cDNA chain; s6, taking the cDNA chain in S5 as a material for constructing an RNA library to obtain the RNA library; wherein S2 is performed on the RNA sample in S1, or S2 is performed after the RNA apparent modification of the RNA sample in S1 is pretreated, or S3 is performed after the RNA apparent modification of the RNA chain in S2 is pretreated. According to the invention, high-throughput detection of a low-initial-quantity RNA sample is realized, and quantitative detection of RNA modification is realized.

The invention discloses a multi-type RNA modification prediction method based on a vector quantization variational auto-encoder, and relates to the technical field of biological information, and the method comprises the steps: obtaining a to-be-detected RNA sequence, and carrying out the preprocessing of the to-be-detected RNA sequence; according to the obtained preprocessing result, performing convolutional coding operation to obtain a feature potential representation; for the feature potential representation, in the trained discrete codebook, determining an embedded vector with the minimum Euclidean distance with the feature potential representation so as to obtain a discrete vector quantization vector; according to the discrete vector quantization vector, adopting a deconvolution decoding operation to obtain a reconstructed RNA sequence; a discrete vector quantization vector is subjected to Transform coding operation containing multiple attention mechanisms, feature vectors are extracted, the probabilities of different RNA modification types are obtained, and therefore the RNA modification types are determined. The accuracy and generalization of prediction are obviously improved, and the biological interpretation of the result is enhanced.

The present disclosure relates generally to methods, compositions, and systems for processing nucleic acids from individual cells or cell populations. The present invention enables direct sequencing of full-length RNA molecules with no amplification steps. The present invention allows determination of RNA modifications in highly specific cell populations of any tissue.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and / or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

This invention discloses a detection method and application for simultaneously acquiring viral integrated transcripts and RNA modifications based on nanopore sequencing. The method includes: obtaining total RNA from a biological sample; separating and purifying the total RNA to obtain mRNA; ligating the mRNA to a reverse transcription adapter; ligating the reverse transcription adapter to a nanopore sequencing adapter; and using strand-specific sequencing, allowing a single-stranded library containing viral integrated mRNA to pass through a nanopore located on a chip without sequencing the complementary cDNA strand, simultaneously detecting viral integrated transcripts and RNA modification information. This method offers the advantages of long-fragment sequencing while simultaneously acquiring base modification information, achieving simple and accurate single-molecule level detection. Furthermore, this method avoids the biases inherent in reverse transcription and PCR, as well as the loss of RNA modification information during reverse transcription and amplification, preserving the natural properties of RNA and obtaining various base variations, structural variations, and modification information, thereby enabling the differentiation of highly similar isoforms and the identification of novel transcripts.

The invention belongs to the technical field of RNA epigenetic modification detection, and discloses an endoplasmic reticulum RNAm6A modification in-situ detection method with subcellular spatial resolution. According to the invention, an endoplasmic reticulum positioning fusion protein (APOBEC1-YTH-KDEL) composed of APOBEC1 deaminase, a YTH m6A recognition domain and a KDEL signal peptide is constructed, and a stable transfection cell system containing an experimental group and multiple controls is established, so that the fundamental limitation that RNA modification space positioning cannot be analyzed in the prior art is overcome. The endoplasmic reticulum targeting of the fusion protein is verified through subcellular co-localization, an endoplasmic reticulum enriched specific m6A editing site is successfully identified on genes such as RABEP1 through sequencing analysis, and the effectiveness of the method is proved. According to the method, in-situ and single-base resolution detection and spatial classification of endoplasmic reticulum RNAm6A modification in a natural living cell environment are realized for the first time, and the method can be widely applied to organelle biological research and toxicity assessment of exogenous stimulation.