322 results about "Chromatin" patented technology

The invention discloses a rice nitrogen response regulation and control network analysis and breeding target identification system and method based on multi-omics data. According to the system, organic combination of regulation and control network construction based on single or multiple varieties of materials, key transcription factor recognition and accurate positioning of regulation and control areas where transcription factors play roles is achieved through an expression-chromatin accessibility correlation research method, and cis-trans effect distinguishing of the regulation and control areas is achieved through a deep learning model. The method comprises the following steps: carrying out nitrogen starvation pretreatment on rice, then carrying out nitrogen resupply, collecting a root sample, and carrying out ATAC-seq and RNA-seq sequencing; an eCAAS method is adopted to construct a regulation and control network, and key transcription factors are identified and accurately positioned; the chromatin accessibility difference of different varieties is predicted through a deep learning model, the cis-action effect and the trans-action effect are distinguished, an upstream transcription factor target is provided for genes dominated by the trans-effect, and haplotype and editable regulatory region targets available for direct breeding are provided for genes dominated by the cis-effect.

The invention relates to the technical field of biology, in particular to a molecular marker for accurately positioning centromere of chromosome of Chinese trumpet creeper, and the sequence of the molecular marker is as shown in SEQ ID NO.1 and SEQ ID NO.2. The method comprises the following steps: specifically enriching a DNA (Deoxyribose Nucleic Acid) sequence combined with a centromere specific histone CENH3 through a chromatin co-immunoprecipitation technology (ChIP), and sequencing the DNA sequence; sequencing data are analyzed to obtain a centromere sequence of the vicia villosa, and two specific repetitive sequences of the centromere of the vicia villosa are obtained after identification and optimization. Primers are designed according to the sequences, PCR amplification is carried out, amplification product sequences are marked, fluorescence in situ hybridization verification is carried out by analyzing a cytogenetics technology, it is proved that the primers are specifically distributed in a centromere area of vicia villosa, and the centromere specificity of the primers is proved. The marker can be used for genetic identification and accurate positioning of the centromere in genome research, and can also be used for cytological identification of the centromere and karyotype research such as chromosome counting and morphological analysis through centromere signal observation.

The invention provides a single-cell multi-omics cell type annotation method based on distribution and knowledge alignment, and belongs to the technical field of single-cell type annotation, the method comprises the following steps: obtaining single-cell transcriptome data and single-cell chromatin accessibility sequencing data, and pre-training and training a multi-omics variation auto-encoder model, the multi-omics variational auto-encoder model is combined with a variational auto-encoder and a knowledge distillation technology, and multi-omics single cell data is integrated and annotated through distribution and knowledge alignment. And performing cell type prediction on the single cell transcriptome data and the single cell chromatin accessibility sequencing data which are input at the same time by using the trained multi-omics variational auto-encoder model. According to the method, the problem of limitation of a method only depending on single omics is solved, the synergistic effect between the omics is enhanced, the accuracy of annotation is improved, and the calculation overhead is reduced through knowledge distillation.

The invention discloses a method for screening molecular markers based on apparent annotation information to carry out whole genome selective breeding, which comprises the following steps: step A, carrying out phenotype determination and genome sequencing on growth traits of a litopenaeus vannamei breeding population to obtain phenotype data and SNP (Single Nucleotide Polymorphism) typing data; step B, performing GS analysis by using phenotype data and SNP typing data, predicting a genome breeding value of a breeding population through a mainstream breeding model, and screening out an optimal breeding model; and step C, classifying chromatin states through ChromHMM analysis by combining the optimal breeding model with the key histone modified region, and screening out the functional SNPs with the key histone modified region. The SNPs have relatively strong functional relevance, are used for different regional groups, and can provide more accurate molecular markers for growth character genetic analysis of bred animals by using less SNPs under the same prediction accuracy, so that the accuracy of genetic breeding value estimation and the cross-group effect are remarkably improved, and the breeding process is accelerated.

The invention relates to a biological information data processing technology, in particular to a method for analyzing a single-cell Hi-C regulation scale chromatin band, which comprises the following steps: preprocessing single-cell Hi-C data to generate pseudo-batch Hi-C data; performing normalization processing on the pseudo batch Hi-C data to extract a Hi-C contact matrix of each chromosome; identifying and detecting false batch strips from the Hi-C contact matrix; projecting the pseudo batch strips to the original single cell Hi-C data to obtain single cell strips; and carrying out quantitative analysis on the single-cell strip in the original single-cell Hi-C data. According to the method, the regulation and control scale chromatin bands with definite endpoints and directivity can be stably identified, and a band set with remarkable statistics is output.

The invention discloses a neural network calculation method and device for gene expression regulation and control analysis, and relates to the technical field of bioinformatics, and the method comprises the steps: obtaining first feature data and second feature data; constructing an input feature comprising a plurality of regulation and control hierarchies; and inputting the input features of the plurality of regulation levels and the second feature data into the target neural network model, and outputting a prediction result of the gene expression state. According to the neural network calculation method provided by the invention, chromatin accessibility and three-dimensional space interaction data are deeply fused through a dynamic routing module, so that the problem of'black box 'which is inaccurate in prediction and difficult to explain in a traditional deep learning model is solved in a mode of explicitly simulating a real biological regulation mechanism; and a key gene regulatory pathway can be accurately identified.

The technology disclosed relates to detecting gene conservation and expression preservation. In particular, the technology disclosed relates to detecting gene conservation and epigenetic signals for a reference genetic sequence in comparison to a variant of the reference genetic sequence at base resolution through the generation of a plurality of alternative representations of the sequence in chromatin form which may represent evolutionary conservation, transcription initiation, or epigenetic signals, mapping the plurality of alternative chromatin sequences to a gene expression alterability classifier to generate a gene expression class prediction for the variant, and mapping the alternative chromatin sequence to a pathogenicity predictor to detect pathogenicity of variants.

The embodiment of the invention provides a gene regulation network inference method and device, a storage medium and electronic equipment. The method comprises the following steps: acquiring a first time sequence corresponding to a target cell type; the first time sequence comprises accessible chromatin sequencing data and single cell transcriptome sequencing data at different first time points; constructing a corresponding first gene regulation network according to the accessible chromatin sequencing data at each first time point; pruning the first gene regulatory network based on single cell transcriptome sequencing data to obtain a second gene regulatory network corresponding to each first time point; and deducing a plurality of second gene regulatory networks corresponding to the first time sequence based on a pre-constructed gene regulatory network prediction model to obtain a target gene regulatory network corresponding to the target cell type at a second time point, the second time point at least comprising a future time point and / or a missing time point in the first time sequence. The method can improve the inference accuracy of the gene regulatory network.

Provided is a hydrogel with a biological material embedded therein, which comprises a core gel material with a biological material embedded therein, the biological material being a biological material subjected to permeabilization treatment. Enveloping biomolecules in a hydrogel and performing permeabilization treatment therein can improve the intensity of permeabilization and compatibility to various bioreactions of the biomolecules. Also provided is a method for constructing a single cell library for the biomaterial in the hydrogel with the biological material embedded therein. The method can be used for library construction for mitochondrial DNAs and / or library construction for open chromatin regions and / or library construction for 3' end transcriptome (RNAs).

Disclosed are compounds that are useful for modulating or degrading protein which is expressed from one or more SWI / SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A (SMARCA) (e.g., SMARCA2 and / or SMARCA4).

Methods of predicting a chromatin state metric associated with a genomic region in a sample are provided. The methods comprise: receiving sequence data comprising genetic data and epigenetic data indicative of the presence of one or more epigenetic bases including methylated cytosine and hydroxymethylated cytosine at one or more genomic positions, the one or more epigenetic bases, the genetic data and epigenetic data obtained from a single assay; and predicting for each base or set of bases of the genomic region and using the sequence data associated with the genomic region, a value of the chromatin state metric, wherein the predicting is performed using a machine learning model.

Metastatic uveal melanomas are highly resistant to all existing treatments. To identify actionable vulnerabilities, the inventors conducted a CRISPR-Cas9 knockout screen using a library composed of chromatin remodelers. They revealed that the histone H3 methyltransferase SETDB1 plays a critical role in metastatic uveal melanoma cell proliferation and survival. Functionally, SETDB1 knockdown triggers decreased expression of genes related to replication and cell cycle and promotes growth arrest associated with increased markers for DNA damage and senescence entry. Using pre-clinical model, they further demonstrated that anti-SETDB1 therapy tumor growth in vivo. The inventors identify SETDB1 as a new relevant therapeutic target for the treatment of metastatic uveal melanomas. The present invention relates to a method for treating uveal melanoma in a subject in need thereof comprising a step of administering said subject with a therapeutically effective amount of SETDB1 inhibitor.

The invention discloses a Rongchang pig T2T genome assembly method. The method comprises the following steps: 1) collecting and sequencing a sample; 2) genome investigation and assembly; 3) genome annotation; wherein in the sequencing step, three sequencing technical means, namely, a three-generation gene sequencing technology PacBio, Nanopore PromethION 48 short reading and chromatin conception capture (HiC), are adopted, and the Rongchang pig genome is subjected to sequencing and sequence splicing together. The Contig N50 value of the genome is nearly three times that of Sscrofa11.1, and the improvement is mainly embodied in a complex genome region (centromere and telomere regions), so that the genome becomes the most complete genome available at present.

The invention discloses a method for detecting accessibility of space chromatin and application of the method. The method comprises the following steps: (1) slicing a tissue sample to be detected on a chip with spatial information; (2) fixing, permeabilizing and dyeing a tissue sample to be detected; (3) preparing fragmented genome DNA (deoxyribonucleic acid); (4) performing DNA hybridization based on a transfer mode; (5) carrying out connection and terminal repair reaction on the fragmented genome DNA by using DNA polymerase and DNA ligase; (6) denaturation and melting; and (7) sequencing. According to the method, the transcriptional activity state of chromatin can be reflected through chromatin accessibility sequencing analysis, staining imaging and chromatin accessibility information can be obtained on the same tissue slice at the same time without complex micro-fluidic equipment, experimental operation is easy, repeatability is high, and the analysis result is more remarkable.

The technology disclosed relates to reliably identifying variants that cause extreme levels of gene expression. Extreme levels of gene expression include under expression and over expression. Then, these variants are used to train artificial intelligence based models for a variety of prediction tasks. One example of the prediction tasks is to produce per-base resolution for chromatin sequences. Another example of the chromatin task is to produce gene expression changes caused by the reliably identified variants.

The invention discloses a method and a kit for RNA-chromatin interaction capture and analysis. According to the present invention, with the adoption of the Mode-specific in situ RNA-chromatin interaction capture technology (MiRCIC) technology, the dual targeting of the specific RNA and the interaction mode during the RNA-chromatin interaction detection process can be achieved, and the dual targeting of the specific RNA and the interaction mode can be further achieved; the F (ab ') 2 fragment is coupled with an oligonucleotide fragment modified by biotin and NH2 to generate the F (ab') 2 fragment-oligonucleotide conjugate, and the F (ab ') 2 fragment-oligonucleotide conjugate is applied to detection, enrichment and analysis of RNA-chromatin interaction. And economic, rapid and high-sensitivity capture, enrichment and analysis on specific interaction mode-mediated and specific RNA-participated RNA-chromatin interaction in a cell in situ can be realized.

The invention belongs to the technical field of biology, and provides a medium-flux single cell four recombinant library construction and sequencing technology mtCOOL-seq (mid-throughput single cell multi-gene sequencing), and the four recombinant library construction and sequencing technology comprises a transcriptome, a DNA (deoxyribonucleic acid) methylation group, copy number variation and chromatin openness. The combination of the omics can comprehensively reveal a gene expression regulation mechanism and a functional state of a single cell. The mtCOOL-seq technology overcomes the defects of scRRBS, iscCOOL-seq and the like in the prior art, integrates the advantages of the scRRBS, the iscCOOL-seq and the like, and provides a more powerful and practical tool for single-cell multi-omics research.

Described herein are conformation capture methods to identify DNA regulatory interactions between accessible chromatin regions. The methods can be used to identify the DNA regulatory interactions of each single cell in a heterogeneous cell population e.g. a tissue or blood sample, and to kits for performing said method. Specifically, the methods relate to identifying DNA regulatory interactions comprising steps of combinatorial indexing and sequencing to separate and analyse the interactions between accessible regulatory regions at individual loci at high resolution for each cell.

The invention provides a method for constructing a single cell library aiming at a biological material in hydrogel embedded with the biological material. The method can be used for carrying out library construction on mitochondrial DNA and / or carrying out library construction on a chromatin open interval and / or carrying out library construction on a 3 '-terminal transcriptome (RNA).

The invention relates to the technical field of biological medicines, in particular to application of categravir or medicinal salt thereof in preparation of tumor treatment medicines. The applicant discovers that the categravir can enable chromatin of tumor cells to be more open, so that DNA of the tumor cells is more easily attacked by chemotherapeutic drugs, more DNA damage is generated, genome instability is caused, the apoptosis number of the tumor cells is further increased, and the development of tumors is inhibited. The mechanism can reduce the dosage of chemotherapeutic drugs, thereby reducing the non-selective damage of the chemotherapeutic drugs to normal tissues and improving the treatment safety. And a new treatment choice is provided for patients who are ineffective in traditional chemotherapy, and the compound is especially suitable for chromatin accessibility abnormality mediated drug-resistant tumors.

The present invention relates to a chromatin open site marker associated with the identification and early screening of high-risk populations for colorectal cancer and its application. The marker is rs10871066. Large-scale population data and biological functional experiments have confirmed that the rs10871066 site has functional regulatory activity, and individuals carrying the rs10871066[A] genotype are more likely to bind to the transcription factor FOXP1, while individuals carrying the rs10871066[G] genotype are more likely to bind to the transcription factor TCF7L2, thereby affecting the chromatin interaction between the region and the promoter of the target gene, promoting the expression levels of the target genes PIBF1 and KLF5, and thus promoting cancer cell proliferation, ultimately leading to an increased risk of colorectal cancer in individuals. By detecting the rs10871066 risk site in normal people, high-risk populations for colorectal cancer can be identified, assisting in the diagnosis of colorectal cancer patients.

Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.

Multi-scale footprinting of DNA-protein interactions is described. Multi-scale footprint scores may be generated based on chromatin accessibility data, the multi-scale footprint scores indicating protein binding to positions of a genome at different protein size scales. A deep learning model may be trained using the multi-scale footprint scores and corresponding DNA sequences. DNA-protein interactions for a DNA sequence of interest may be predicted using the trained deep learning model. The prediction may include generating sequence attribution scores for the DNA sequence of interest using the trained deep learning model and predicting transcription factor binding sites of the DNA sequence of interest based on the sequence attribution scores.

A method for predicting a CTCF chromatin loop on the basis of a transcription factor sequence in a loop extrusion model, comprising: constructing a data set; converting a key transcription factor sequence; establishing a CTCF chromatin loop classification model on the basis of the key transcription factor sequence; and evaluating the model. In the method, a transcription factor binding order is encoded into a transcription factor sequence, and the transcription factor sequence is decoded by utilizing a pre-trained natural language BERT model, thereby achieving the prediction of the CTCF chromatin loop. The method not only improves the prediction accuracy but also enhances the interpretability of a predictive model.

This invention belongs to the field of plant genetic engineering technology, specifically relating to the application of H3K27me3 in regulating the cotton response to potassium chloride stress. By integrating CUT & Tag chromatin analysis and RNA-seq, this invention demonstrates that potassium chloride stress induces a reduction in H3K27me3 deposition across the entire genome, accompanied by characteristic stress phenotypes in cotton seedlings. Inhibition of H3K27me3 using RDS 3434 significantly improved KCl-induced physiological damage, confirming the functional correlation between this epigenetic marker and stress tolerance. Furthermore, virus-induced gene silencing confirmed that genes associated with H3K27me3 are important components of the cotton ion stress response network. Therefore, this invention elucidates the epigenetic landscape regulating adaptation to potassium chloride stress.

The present invention provides compounds, pharmaceutically acceptable compositions thereof, and methods of using the same for the modulation of one or more SWI / SNF-related matrix associated actin dependent regulator of chromatin subfamily A (SMARCA) and / or polybromo-1 (PB-1) protein via ubiquitination and / or degradation by compounds. The compounds are bifunctional molecules that link a cereblon-binding moiety to a ligand that binds SMARCA and / or PB1 proteins.

The invention discloses an application of SNF2 protein derived from streptococcus angina extracellular vesicles in gastric cancer prognosis. The chromatin remodeling protein SNF2 derived from S.anginosus EVs can be combined with a transcription factor TEAD1, so that the transcription of the palmitoyl transferase ZDHHC11 is promoted together. Then, the stability of the ZDHHC11 is enhanced by catalyzing palmitoylation of PD-L1, and finally immune escape is induced. In addition, SNF2 also can activate AXL, CTGF, CYR61 and other carcinogenic targets at the downstream of TEAD1, thereby further accelerating the malignant progression of gastric cancer. In an in-vivo experiment, the intragastric administration of the S.anginosus EVs not only promotes the tumor growth of mice, but also significantly inhibits the infiltration of CD8 + T cells. Blocking of ZDHHC11 can effectively reverse immune escape, and has a synergistic effect with an anti-PD-1 therapy, so that the treatment effect is remarkably improved.

The invention belongs to the field of gene data processing, and provides a chromatin interaction prediction method and system based on dynamic word segmentation and word embedding. The method comprises the steps that DNA sequence information of a data sample is obtained, dynamic word segmentation processing is conducted on the DNA sequence information according to the size of a set vocabulary, and then two labeled subsequences are obtained according to the length and the occurrence frequency of words; converting all the labeled subsequences of the data sample into DNA sequence features through an embedded layer; fusing the known genome characteristics of the data sample with the DNA sequence characteristics to generate joint characteristics; and obtaining chromatin interaction prediction results of the sub-models based on a relationship between the joint features and the chromatin interaction prediction results of the sub-models in the integrated learning model, and averaging the chromatin interaction prediction results to obtain a final chromatin interaction prediction result.

The invention discloses an efficient extraction method of blue fox sperm DNA, and belongs to the technical field of molecular biology. Aiming at the structural characteristics that chromatin of the blue fox sperms is highly condensed, histone is replaced by protamine, and a stable nucleoprotein complex is formed through an intermolecular disulfide bond, the invention provides an efficient DNA extraction method suitable for the blue fox sperms. According to the method, based on the synergistic effect of three chemical reagents, namely SDS, PK and DTT, full lysis of the sperm cells of the blue foxes is achieved, and then efficient enrichment of sperm DNA of the blue foxes can be achieved by combining a conventional DNA extraction method. According to the efficient extraction method of the blue fox sperm DNA provided by the invention, the yield and integrity of the blue fox sperm DNA are remarkably improved, and the limitation that sperm chromatin is difficult to effectively lyse by a conventional method is overcome; the method provides reliable technical support for research on genetic diversity evaluation, population management, molecular breeding and the like of the blue foxes, and has the potential of popularization and application in other high-condensation sperm species.

The present invention discloses a method and system for mining potential proto-oncogenes based on the three-dimensional structure of chromatin, which relates to the field of computational biology technology. The method comprises: obtaining multiple mutation insulation regions based on chromatin data and cancer mutation data, and inputting the regions into a trained binding site predictor to obtain prediction results and destroyed insulation regions; obtaining multiple differentially expressed gene sets based on cancer gene expression data, intersecting the multiple differentially expressed gene sets to obtain a final differentially expressed gene set; intersecting the final differentially expressed gene set and the genes in the destroyed insulation regions to obtain intersection genes; performing survival analysis to obtain analysis results, screening the intersection genes based on the analysis results to obtain genes associated with poor prognosis; and screening the intersection genes to obtain potential proto-oncogenes. This improves the accuracy and reliability of mining potential proto-oncogenes while saving time and economic expenses.