19 results about "Centromere" patented technology

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.

Described herein are artificial centromeres and artificial chromosomes comprising the artificial centromeres and a cargo sequence, methods of designing and making such artificial centromeres and artificial chromosomes, cells comprising such artificial centromeres and artificial chromosomes, and methods of using such artificial centromeres and artificial chromosomes for stable passaging of artificial chromosomes and expression of cargo sequences in a mammalian cell.

The invention discloses a centromere sequence extraction and chromosome classification method and a related device, and belongs to the technical field of bioinformatics. The method comprises the following steps: acquiring a second-generation sequencing sequence data file and a corresponding reference genome sequence file, and segmenting the second-generation sequencing sequence data file into N sub-files according to a set parallel thread count; creating N parallel thread units, extracting feature vectors of the sequencing sequences in the N sub-files by adopting a DNA sequence feature extraction model, inputting the feature vectors into a pre-constructed centromere sequence recognition model, and screening out candidate centromere sequences; and converting each candidate centromere sequence into a feature vector by using the DNA sequence feature extraction model, and inputting the feature vector into a pre-constructed chromosome classification model to obtain a chromosome attribution result. According to the method, by combining data parallel preprocessing, machine learning and a deep learning model, the centromere region sequence can be identified in large-scale massive next-generation sequencing data, and the chromosome to which the centromere region sequence belongs can be further predicted.

The invention belongs to the technical field of biological information, and discloses a plant centromere identification and boundary defining method, which specifically comprises the following steps: carrying out quality control on CENH3 ChIP-seq original sequencing data; comparing the reads after quality control to a target plant reference genome, calculating the average coverage or ChIP signal of each bin according to a preset window after file conversion, and generating a CENH3 distribution curve; identifying a CENH3 binding peak region by using signal enrichment analysis software; and selecting a section of which the continuous strength is higher than a preset threshold value as a core centromere, extending towards two sides at a fixed step length until the signal strength is lower than the preset threshold value, determining the starting and ending positions of the boundary, and outputting. According to the plant centromere recognition and boundary defining method, automation and repeatable recognition of a centromere area are achieved, the boundary resolution and accuracy are improved, the method is suitable for double plants, and a reliable tool is provided for chromosome structure research and crop breeding.

The disclosure provides for methods of constructing synthetic chromosomes including the steps of providing host cells with an endogenous chromosome, transforming a cloning vector and a cloning cassette into the host cells, excising target genomic nucleic acids from the endogenous chromosome, recombining the excised target genomic nucleic acids with the cloning cassette via homologous recombination to form heterologous vectors comprising cloned sequences, extracting the heterologous vectors containing the cloned sequences from the host cells, digesting the heterologous vectors with a restriction endonuclease to release the cloned sequences from the heterologous vectors to provide released cloned sequences, and introducing the released cloned sequences, a centromere cassette, and a yeast artificial chromosomes or bacterial artificial chromosomes into a second host cell, such that the released cloned sequences, the centromere cassette, and the YAC or BAC recombine with one another via homologous recombination to produce the synthetic chromosome.

Compositions and methods for deleting a target DNA sequence from a target DNA molecule are provided. The disclosed GRAND-Del system employs a pair of pegRNAs that target nearby genomic sites and have mutually complementary sequences to jointly form a template for inserting an exogenous sequence into a target DNA molecule to replace a target DNA sequence to be deleted. The deleted chromosomal DNA sequence can be degraded, randomly inserted (resulting in random transposon), or inserted at a target location, such as at different locations of the same chromosome or in different chromosomes (resulting in targeted transposon) or in centromere-containing plasmids (resulting in the production of artificial chromosomes).

The invention discloses a peanut chromosome centromere specific molecular marker and application thereof, particularly relates to the technical field of molecular cytogenetics, and aims to solve the technical problem that peanut chromosome centromere is difficult to accurately recognize in the prior art. According to the specific molecular marker of the peanut chromosome centromere, the molecular marker comprises CentAh106 or CentAh342; the nucleotide sequence of the CentAh106 is as shown in SEQ ID NO. 1, and the nucleotide sequence of the CentAh342 is as shown in SEQ ID NO. 2.

The invention discloses an identification method of a sequence participating in potato centromere relocation, and belongs to the technical field of plant heredity and molecular biology. According to the method, T2T-level genome data and CENH3 ChIP-seq data of different haplotypes of potatoes are integrated, sequence screening, annotation and function prediction are carried out by utilizing a bioinformatics analysis tool, and a satellite DNA sequence which is 2-3Kbp in length, is highly conserved in the same haplotype and can be specifically combined with CENH3 protein is identified. The sequence can induce CENH3 to deposit in a non-native centromere area, so that functional relocation of centromere is realized, and a core molecular element and a technical support are provided for artificial centromere construction, plant chromosome engineering and accurate genome operation. The method solves the problems that in the prior art, a functional sequence for clearly inducing centromere relocation is lacked, a CENH3 targeted recruitment mechanism model is not established and the like, and has a wide application prospect.

The invention relates to a breast cancer HER2 gene and muscle epithelium marker synchronous detection fluorescence double-staining kit and a method thereof. The double-staining kit comprises a HER2 gene specific fluorescence labeling probe and a CEP17 centromere probe; an anti-CK5 / 6 antibody and a corresponding fluorescently-labeled secondary antibody; the EDTA buffer solution is used for antigen repair; the invention discloses a dyeing buffer solution capable of ensuring double dyeing compatibility. The method is suitable for accurate detection of breast cancer samples with limited infiltration components in a dark field, synchronous analysis of HER2 genes and myoepithelium markers on the same slice is realized, the problems of inaccurate positioning, low efficiency, specimen waste, treatment delay and the like in the existing FISH detection technology are solved, and the method has the advantages of improving the detection accuracy, improving the efficiency, reducing tissue consumption, reducing the cost and the like. And the clinical application potential is improved.

The present application belongs to the field of biotechnology and medicine, and relates to a centromere binding protein Cbf1, a coding gene thereof and application. Specifically, the present application provides a Cryptococcus virulence related protein, which is a centromere binding protein Cbf1. Meanwhile, the present application also provides application of the centromere binding protein Cbf1 in preparation of a medicine, CBF1 Gene knockout leads to reduction of tolerance of the strain to 37 DEG C, oxidation and cell wall pressure, and reduction of melanin production, so that the protein can be used as a drug target and applied to research and development of a new drug for treating diseases caused by Cryptococcus.

The invention discloses a yarrowia lipolytica expression vector and application thereof, and particularly discloses a nucleic acid molecule C-M6, and the DNA sequence of the nucleic acid molecule C-M6 is SEQ ID NO: 23; the invention also discloses a vector containing the nucleic acid molecule, the vector comprises the following elements: centromere, an autonomous replication sequence, a resistance gene, a promoter, a selection marker gene and a terminator, and the centromere is the nucleic acid molecule in claim 1. The nucleic acid molecule provided by the invention is used as a centromere in a yeast carrier, and compared with a traditional carrier carrying ARS and a carrier carrying a wild type centromere sequence, the constructed yeast carrier has higher stability and can be used for expressing target protein to obtain higher protein expression yield.

The invention discloses a preparation method of chromosomes of tiny insects trichogramma dendrolimus, and belongs to the technical field of chromosome preparation. Comprising the following steps: (1) preparing a pre-pupa material: selecting corcyra cephalonica eggs parasitized by trichogramma dendrolimus for 4-8 days, and cutting out a trichogramma dendrolimus pre-pupa; (2) pretreatment: pretreating the pre-pupa material in a colchicine solution; (3) low-permeability treatment: carrying out low-permeability treatment on the pretreated material in a low-permeability solution; and (4) fixing, uncovering, dyeing and sealing the material subjected to the low-permeability treatment. The invention provides a simpler trichogramma dendrolimus chromosome slide preparation method, chromosome slides with clear forms can be prepared in batches, the dispersion degree of chromosomes is large, the length, centromere position, arm ratio and other characteristics of the chromosomes can be observed more clearly, the chromosome characteristics are determined through karyotype analysis, and the chromosome slide preparation method is suitable for large-scale production. And a foundation is laid for cell level research and genomics deep research of trichogramma dendrolimus.

The invention relates to a centromere sequence alignment method based on phylogenetic information and pairing editing distance, and belongs to the technical field of centromere sequence alignment. According to the algorithm provided by the invention, a collinearity relation is constructed by utilizing phylogenetic information of a satellite sequence and a pairing editing distance. According to the method, firstly, a conservative selection mode is adopted, and an editing distance (ED) threshold value is gradually increased until a collinear framework between two sequences covers more than 20% of the total number of monomers or 100 monomers; according to the method, an ordered chain with the highest comprehensive score is identified through DAGchainer software according to sequence homology and genome coordinates by integrating the physical distance between adjacent elements, the sequence and the E value score of BLAST, and a collinear satellite region is constructed. Then, a sliding window strategy is adopted, 20 collinear satellite pairs serve as a window, sub collinear satellite areas are recognized, and therefore the analysis precision is effectively improved, and local satellite collinear pairs are supplemented by widening an editing distance (ED) threshold value.

This invention belongs to the field of genomics and bioinformatics technology, specifically relating to a method for multidimensional quality assessment of telomere-to-telomere genomes. The method includes the following steps: preprocessing the genome data to be assessed to obtain preprocessed data; quantitatively assessing multiple core features of the preprocessed data, including accuracy, completeness, continuity, and region specificity; the region specificity includes telomere identification, centromere identification, and collinearity with a reference genome; calculating a comprehensive score based on the weighted results of the quantitative assessment of the core features, and using the comprehensive score to determine the quality of the genome to be assessed. This assessment method is specifically adapted to the core features of T2T genomes, taking into account continuity, completeness, accuracy, and region specificity, thus solving the problem that traditional methods cannot assess T2T-specific features.

Described herein are artificial centromeres and artificial chromosomes comprising the artificial centromeres and a cargo sequence, methods of designing and making such artificial centromeres and artificial chromosomes, cells comprising such artificial centromeres and artificial chromosomes, and methods of using such artificial centromeres and artificial chromosomes for stable passaging of artificial chromosomes and expression of cargo sequences in a mammalian cell.

The invention discloses an in-vivo protein-DNA interaction analysis method based on methylated DNA immunoprecipitation, and belongs to the technical field of molecular biology. According to the method, an instantaneous protein binding event is recorded as stable 6mA, MeIP captures interaction which cannot be detected by ChIP, and meanwhile, the sequence background limitation of DamID is avoided. The compatibility with qPCR and sequencing enables the experiment scale to be flexibly adjusted, and the simple implementation of the method enables the method to be very suitable for researching related proteins interacting with chromatin in organisms lacking endogenous DNA methylation. The invention also discloses the transient but critical localization of a kinase at the centromere, and emphasizes the necessity of capturing a dynamic chromatin event for understanding genome regulation. The MeIP technology can be applied to a mammalian cell system, and a powerful tool is provided for researching instantaneous chromatin regulation events in higher eukaryotes.

The application discloses a kind of crop centromere automatic identification method, belong to crop centromere identification field, comprising: according to the verified CENH3 binding area sequence and random non-centromere area sequence constructs training set;According to the multidimensional feature of DNA sequence extracted from training set;According to the multidimensional feature training CNN-RNN hybrid model and obtains the prediction model for identifying centromere;According to the prediction model, the target genomic sequence is identified, and the candidate centromere region is obtained.The application no longer depends on repeat sequence, but directly uses CENH3 binding feature, improves prediction accuracy.And can be applied across species, improve the universal applicability of centromere region identification.

This invention discloses the identification, construction, and application of plant centromere tandem repeat sequences. The method includes: obtaining the target plant genome sequence; detecting tandem repeats through prefix sum vectorization to obtain candidate repeat regions and periods; extracting repeat units as candidate monomers and eliminating low-complexity noise; calculating a multi-feature fusion score for candidate monomers, the score including period consistency, genome enrichment, sequence complexity, and GC content shift, and screening based on the score; clustering the screened candidate monomers to obtain monomer subtypes; performing phase correction on monomers within subtypes; and constructing a consensus sequence based on the corrected sequence. This application achieves quantitative evaluation of centromere attribution probability through multi-feature fusion scoring, combined with exhaustive cyclic shift phase correction, to obtain a consensus sequence without relying on external tools or known motifs. Taking the Arabidopsis Col-CEN genome as an example, the optimal period is 178 bp, the column consistency rate is 0.9272, and the alignment consistency with the reference sequence exceeds 98%.

The application discloses a design method and application of a pig chromosome telomere probe, and belongs to the technical field of molecular biology. The application uses a bioinformatics method to screen a pig chromosome telomere probe with high repetition and high specificity from preliminary searching and comparison. The nucleotide sequence of the pig chromosome telomere probe is shown as SEQ ID NO. 1. The application uses a pig primary cell line and an immortal cell line to develop an in-situ fluorescence hybridization pre-preparation reagent, and the results show that the probe can be combined with a current DNA region better. The design method of the pig chromosome telomere probe can be used for the design of most probes, the developed pig chromosome telomere probe has high specificity, good hybridization effect and high detection accuracy, and provides a new perspective and method for in-depth research on pig chromosome rearrangement and translocation.