57 results about "Transcription start" patented technology

The invention discloses application of a gene marker in early screening of esophagus, stomach and intestine multiple cancer species, an early screening model construction method and a detection device, and belongs to the technical field of early noninvasive detection of digestive tract tumors. By analyzing the whole genome characteristics of circulating free DNA in peripheral blood, a novel multi-cancer-species screening system is established. On the basis of low-depth whole genome sequencing data, molecular markers in three dimensions, namely a genome copy number variation mode, a DNA fragment distribution characteristic with a specific length and an epigenetics signal of a transcription initiation region, are emphatically detected. An advanced converter neural network architecture is adopted, and the model can efficiently capture complex feature association in a whole genome range through a specific self-attention mechanism. The model design particularly considers the particularity of genome data, introduces an adaptive position coding system, and accurately reflects the spatial distribution relationship of DNA fragments on chromosomes. Therefore, the system can still maintain excellent detection performance under extremely low sequencing depth.

The invention relates to the technical field of gene engineering, in particular to application of a knock-down CDYL gene in improvement of cattle meat production performance. The invention provides an application of knocking down a CDYL gene in improving the differentiation capacity of cattle muscle satellite cells and / or improving the meat production performance of cattle. The gene ID of the CDYL gene is 539013. The 404th basic group A on the upstream of the CDYL gene transcription start site is deleted through a gene editing method, so that the CDYL knock-down gene editing cattle is created, compared with wild cattle and gene editing cattle, the myotube forming ability of muscle satellite cells is obviously enhanced, the number of myotube marker intermuscular line protein positive cells is obviously increased, the number of multinuclear myotubes is obviously increased, and the CDYL knock-down gene editing cattle has the advantages that the CDYL knock-down gene editing cattle can be used for preparing the CDYL knock-down gene editing cattle. And the weight and body size data (body height, cross height, body oblique length, chest circumference and abdominal circumference) of the gene edited cattle are greater than those of the wild cattle. According to the invention, high-yield breeding genes of beef cattle are enriched, and technical support is provided for cultivation of novel gene editing animals.

The invention discloses an InDel molecular marker related to seedless traits of filial generations of grapes and application of the InDel molecular marker. The nucleotide sequence deletion part of the InDel molecular marker for the seedless type of the filial generation of seedless grape and nucleated grape is shown as SEQ ID NO.3, and is positioned at the upstream 263-693 bp of a VviAGL11 gene transcription start site (TSS) which is closely linked with the seedless character of the grape, and the nucleotide sequence deletion part of the InDel molecular marker is shown as SEQ ID NO.6. The nucleotide sequence deletion part of the InDel molecular marker is shown as SEQ ID NO.7. The nucleotide sequence deletion part is shown as SEQ ID NO.8. According to the invention, PCR (Polymerase Chain Reaction) amplification and Sanger sequencing are carried out on VviAGL11 gene promoters of a seedless grape variety 'Zhongqing 18' and a seedless grape variety 'Musang', so that polymorphic sites with significant difference are obtained, and the difference between the polymorphic sites is 431 bp. The InDel molecular marker is suitable for grape seedless molecular marker-assisted selective breeding, and the invention also discloses a method for carrying out genotype identification through an agarose electrophoresis technology in a seedling stage of hybrid generations of seedless grapes and seedless grapes, so that early selection of seedless characters of the grapes is realized; the seedless grape breeding efficiency is further improved, the breeding cost is reduced, and the breeding process is promoted.

The invention discloses a plukenetia volubilis FAD2 gene promoter. The nucleotide sequence of the plukenetia volubilis FAD2 gene promoter proPvFAD2.4 is shown in the specification. The proPvFAD2.4 comprises TATA-box and CAAT-box, and the TATA-box and the CAAT-box are located at the upstream of a transcription start site (TSS), so that basic transcription support is provided for positioning of RNA polymerase II, and the basic expression level of the gene is ensured. Comprising seed specific elements of AE-box and O2-site, and specific expression of PvFAD2 in the seed development stage is combined with DOF (OBP2) and MADS-box transcription factors to drive grease to be quickly accumulated. And the recombinant plasmid vector has a strong starting effect, so that the promoter has a function of starting downstream gene expression in a tobacco leaf cell environment, and an experimental foundation is laid for subsequent analysis of a regulation mechanism of the promoter.

The application belongs to the technical field of biological gene engineering, and particularly relates to a barley HvCslf6 promoter element and application thereof in regulating the content of barley grain beta-glucan, wherein the barley HvCslf6 promoter element is located at 295bp-300bp upstream of a transcription start site of a barley HvCslf6 gene; the nucleotide sequence of the HvCslf6 promoter element is CCGTTG, and the HvCslf6 promoter element belongs to a CCAAT-box element; the gene number of the HvCslf6 gene in BARLEX Morex v3 Gene Models is HORVU.MOREX.r3.7HG0698110. The application finds a key element which can affect the content of beta-glucan in barley grains in the upstream promoter region of a main effect gene HvCslf6 of barley beta-glucan synthesis by using a gene editing technology, and thus provides a method capable of preparing transgenic plants with changed content of beta-glucan in barley grains, and provides a new means and tool for detecting and regulating the content of beta-glucan in barley grains.

The integration procedure provides different elements that require in vitro amplification of HSPCs, preferably for about 48 hours, in the presence of hematopoietic cytokines as well as UM171 and stem cell regenerative factor 1, and the introduction of i) a system (e.g., a CRISPR / Cas9 system) that generates DNA double-strand breaks (DSBs) upstream of the transcription start site of the target gene, and ii) the introduction of a donor matrix comprising cDNA with homologous arms on both sides (left [LHA] and right [RHA]).

Methods for increasing expression of a target gene, the method comprising introducing a CCCTC-binding factor (CTCF) binding site (CTCF-BS) into a promoter region of the target gene, e.g., within 500, 250, 200, 150, 100, 50, or 25 nucleotides of the transcription start site (TSS) for the target gene, and optionally expressing in or introducing into the cell a CTCF protein or variant thereof.

The present invention relates to the field of genetic engineering technology, and particularly to the application of knocking down CDYL genes in improving the meat production performance of cattle. The present invention provides the application of knocking down CDYL genes in improving the differentiation ability of bovine muscle satellite cells and / or improving the meat production performance of cattle, and the gene ID of the CDYL gene is 539013. The present invention deletes the 404th base A upstream of the transcription start site of the CDYL gene by gene editing, thereby creating a CDYL gene-edited cattle with knocked-down gene. Compared with wild-type cattle, the myotube formation ability of muscle satellite cells in gene-edited cattle is significantly enhanced, the number of desmin-positive cells, a myotube marker, is significantly increased, the number of multinucleated myotubes is significantly increased, and the body weight and body size data (body height, rump height, body slant length, chest girth and abdominal girth) of gene-edited cattle are all greater than those of wild-type cattle. The present invention enriches the breeding genes for high-yield beef cattle and provides technical support for the cultivation of new gene-edited animals.

The invention relates to the field of gene engineering, in particular to a cascade reaction-based plasmid elimination module, which comprises three types of mutually independent expression regions, one type of the expression regions is an antisense RNA expression region and comprises antisense RNA, a promoter of the antisense RNA and a terminator, and the other type of the expression regions is an antisense RNA expression region and comprises antisense RNA, a promoter of the antisense RNA and a terminator of the antisense RNA. The antisense RNA is the antisense RNA of a metabolic key gene mRNA, and can be combined with the metabolic key gene mRNA to hinder the translation of the metabolic key gene mRNA; the first region is an antisense neutralizing RNA expression region and comprises antisense neutralizing RNA, an inducible promoter of the antisense neutralizing RNA and a terminator of the antisense neutralizing RNA; the last type of region is a transcription factor region and is composed of constitutive promoters carried by a transcription factor fragment, and the constitutive promoters comprise an RNA polymerase binding site, a transcription start site, a ribosome binding site, a transcription factor translation region and a terminator; the antisense neutralizing RNA is an RNA fragment which is complementary with the antisense RNA in sequence, can be combined with the antisense RNA to enable the antisense RNA not to be combined with the metabolic key gene mRNA, and inhibits the antisense RNA from generating translation obstruction on the metabolic key gene mRNA. The method is high in elimination efficiency, elimination objects can be freely set according to needs, and selective or synchronous elimination of various plasmids can be realized.

The invention relates to a cancer non-invasive early screening method and system based on sequencing coverage depth and fragment size characteristics near a cfDNA transcription start site.

The application provides a non-coding mutation-induced risk gene expression up-regulation and down-regulation prediction method and system, comprising the following steps: step 1, obtaining a data set and performing pretreatment; step 2, information input standardization between non-coding mutations and gene transcription start points TSS; step 3, non-coding mutation information input standardization; step 4, sequence length alignment and representation learning framework; and step 5, embedded feature merging and prediction output. The application is matched with chromatin accessibility sequencing data to migrate to any tissue or cell type, make accurate and reliable prediction, and utilize an attention mechanism to endow the model with interpretability.

The invention discloses a multi-reporter gene expression cassette for plant promoter expression pattern and activity analysis, the expression cassette sequentially comprises a multiple cloning site MCS and a terminator from 5'end to 3 'end, at least two reporter genes are arranged between the MCS and the terminator, and the adjacent reporter genes are spaced by a 2A sequence, the reporter genes are different types of reporter genes, the types of the reporter genes include but are not limited to fluorescent protein reporter genes and enzyme reporter genes, the 2A sequence is a 2A self-cleavage peptide sequence, and the terminator has the capability of terminating transcription started by the Pol II type promoter. The MCS in the expression cassette facilitates cloning of various promoters and other functional elements, and the expression cassette contains fluorescent protein reporter genes and enzyme reporter genes at the same time, has the advantages of the fluorescent protein reporter genes and the enzyme reporter genes, and has the advantages of being wide in application range and diverse in detectable means.

The invention provides a separated Actin5C promoter as well as a construction method and an expression vector thereof, the separated Actin5C promoter is a partial region of a wild Actin5C promoter, and the partial region comprises a region from the 94th site in the downstream direction of a transcription start site to 400bp-600bp in the upstream direction. The separated Actin5C promoter is short in length, so that the expression vector containing the Actin5C promoter is small in size and high in transfection efficiency. By utilizing the expression vector provided by the invention, the target protein yield of in-vitro insect S2 cells can be remarkably improved, and the scientific research and clinical application values are high.

Guide RNAs and CRISPR / Cas systems targeting a C9orf72 gene, lipid nanoparticles or viral vectors comprising such CRISPR / Cas systems, and cells or animals comprising such CRISPR / Cas systems are provided. Methods of repressing transcription from a C9orf72 exon 1 A transcription start site and / or repressing transcription of sense and / or antisense transcripts that comprise the hexanucleotide repeat expansion sequence in a C9orf72 gene using the CRISPR / Cas systems are also provided, as well as use of the CRISPR / Cas systems in prophylactic and therapeutic applications for treatment and / or prevention of a C9orf72 hexanucleotide repeat expansion associated disease and / or for ameliorating at least one symptom associated with such disease.

The application discloses an application of a leucine-rich repeat receptor-like kinase gene of Gossypium anomalum, which is composed of 3885 bases, wherein the first base from the 5' end is a transcription start site, and the 3885th base is a transcription termination site. Expression of the gene can cause a lethal phenotype of a single segment introgression line CSSL11-9 of the Gossypium anomalum. The lethal phenotype is inhibited by silencing the gene expression in the single segment introgression line CSSL11-9 of the Gossypium anomalum, and the single segment introgression line CSSL11-9 can survive normally. In addition, the gene can also endow cotton with resistance to verticillium wilt and fusarium wilt, and the resistance of the CSSL11-9 plant with the silenced gene to the cotton verticillium wilt and fusarium wilt is significantly reduced, thereby providing an important gene resource for cotton breeding against the verticillium wilt and the fusarium wilt.

Provided are a tissue tracing method for cell-free DNA, a tissue lesion risk notification method, a cell-free DNA-based cancer risk indication method, a cell-free DNA-based gestational disease risk indication method, a cell-free DNA-based receptor tolerance risk notification method, a disease treatment effect evaluation or prognosis method and apparatus, an electronic device, a computer-readable storage medium, a computer program product and a computer program. The tissue tracing method for cell-free DNA comprises: acquiring a tissue-specific expression gene set of a tissue; acquiring first distribution information of cell-free DNA derived from a sample on specific regions of genes in the tissue-specific expression gene set; and, on the basis of the first distribution information, acquiring a tissue contribution index of the tissue in the cell-free DNA, so as to trace the tissue of the cell-free DNA, wherein the specific regions comprise transcription start site (TSS) regions.

This invention belongs to the field of plant molecular biology and genetic breeding technology, specifically relating to a molecular marker related to the malic acid content of apple fruit and its application. The molecular marker is... MdNAC029 The single nucleotide polymorphism site in the gene promoter region, this site is located MdNAC029 The nucleotide sequence of the gene promoter region, starting from the 2693rd base at the 5' end, corresponds to... MdNAC029 At a position 442 bp upstream of the transcription start codon, the polymorphism is either T or C, with the C / C genotype indicating high malic acid content and the T / T genotype indicating low malic acid content. This invention, through molecular biology experiments, confirms that the T allele is the binding site for the transcriptional repressor MdMYC2, and the C allele eliminates the binding of MdMYC2, thereby relieving transcriptional repression and promoting malic acid accumulation. This provides a new molecular marker for the genetic improvement of apple fruit acidity traits, accelerating the breeding process of superior varieties.

The invention belongs to the technical field of biology, and relates to a false cyclization structure for improving mRNA stability in prokaryotes. Through the design of the expression cassette, the tail of the 3'end of the transcribed mRNA has a section of pseudo-cyclization structure which can form complementary pairing with a 5 '-end transcription starting region to form double chains. The false cyclization structure can increase the expression quantity of the target protein by increasing the stability of mRNA (messenger Ribonucleic Acid). The method can be applied to the field of RNA production and recombinant protein expression in prokaryotes, the yield of target RNA and target protein can be increased, so that the production cost is reduced, and the method has relatively high popularization value.

The invention relates to a CD34 + cell pre-stimulation method for realizing clinical related gene editing frequency. Specifically, the present invention relates to different elements of an integrated procedure that entails the ex vivo amplification of HSPC, preferably about 48 hours, in the presence of hematopoietic cytokines, as well as UM171 and stem cell regeneration 1, and introduces i) a system (e.g., CRISPR / Cas9 system) that produces a DNA double strand break (DSB) upstream of the transcription initiation site of the target gene, and i) a system (e.g., CRISPR / Cas9 system) that produces a DNA double strand break (DSB) upstream of the transcription initiation site of the target gene. And introducing ii) a donor matrix comprising cDNA having homologous arms on both sides (left [LHA] and right [RHA]).

The present invention discloses a sequencing method for the dynamics of whole-gene nascent transcription; the present invention uses 4sU to label nascent RNA, improves RNA fragmentation and direct connection of adapters, and an RNA extraction method without length preference, so that short RNA fragments can be retained to the greatest extent, thereby improving the integrity and accuracy of sequencing data; through optimized experimental processes and methods, the present invention can effectively display the transcription dynamics including the downstream of the transcription start point, solving the problem that the transcription dynamic process near the transcription start point in the prior art cannot be accurately reflected; thereby providing a reliable sequencing method for measuring the early dynamics of transcription. Moreover, the present method can identify genes with rapid stress response, reveal early transcription events such as early termination of transcription; it can also be used to understand the dynamic changes of gene expression in the disease process, reveal the pathogenesis of the disease, and provide tools for related targeted drug research.

The present inventors found an inhibitory neuron-specific promoter sequence which, although having a shorter length than the mGAD65 promoter, does not impair any of the promoter activity, specificity for inhibitory neurons, and gene expression efficiency, which is specifically a promoter consisting of DNA having a promoter activity, comprising: a base sequence of a Dlx1 binding site and / or a Dlx2 binding site in a glutamic acid decarboxylase (GAD) promoter; and a base sequence of a region ranging from a 5′ end of exon 1 to a transcription start site (TSS) in a glutamic acid decarboxylase (GAD).

The invention relates to a sample treatment method for detecting accessibility of single cell chromatin and application of the sample treatment method. The sample treatment method comprises the following steps: slicing a tissue sample to obtain a tissue slice, and sequentially carrying out permeabilization treatment, transposase treatment and cell nucleus extraction treatment on the tissue slice, the tissue sample includes a frozen tissue sample. According to the method, a'slice in-situ transposition reaction 'strategy is designed, the original spatial conformation and physiological state of chromatin in vivo are effectively maintained, chromatin structure disturbance caused by early release of cell nucleuses in the thawing process is avoided, the quality of ATAC-seq data is remarkably improved, and the method is suitable for being used in a large scale. The enrichment fraction of the transcription start site and the proportion result of fragments overlapped with peaks are remarkably improved, a nucleosome positioning signal is clearer, and the accuracy and reliability of chromatin openness detection are improved.

The present invention relates to a rice bundle sheath cell-specific promoter and its application, belonging to the technical field of agricultural genetic engineering. The nucleotide sequence of the promoter is shown in SEQ ID NO. 1. Through single-cell sequencing and RNA in situ hybridization analysis of rice leaves, the present invention screened and identified a rice bundle sheath cell-specifically expressed gene, Os07g0683900. The 1.5 kb sequence preceding the transcription start site of this gene and the 5' UTR sequence following the transcription start site were selected as the promoter sequence. Analysis of OsSWEET13-overexpressing rice plants driven by this promoter revealed that the rice bundle sheath cell-specific promoter can significantly promote rice growth, providing important theoretical significance and application value for rice breeding.

The present invention is directed to the different elements that integrate a procedure that shall require the ex vivo expansion of HSPCs for, preferably, about 48 hours in the presence of hematopoietic cytokines as well as UM171 and Stemregenin 1 and the introduction of a i) system to generate the double strand breaks of the DNA (DSBs), such as the CRISPR / Cas9 system, upstream of the transcription start site of a target gene, and ii) the introduction of a donor matrix that includes a cDNA flanked by homology arms (Left [LHA] and right [RHA]).

An engineered nucleic acid for regulating levels of gene expression, including in cells is provided. The nucleic acid has a regulatory region with a transcription factor binding site upstream of a transcription start site and separated by a spacer and includes at least one of multiple distinct transcription factor binding sites, a recombination regulation system and / or nested excisable spacers and orthogonal recombination sites. Methods of regulating gene expression are also provided.

The present invention provides a bovine FTO gene promoter mutation site and its application, belonging to the fields of biotechnology and genetic engineering. This mutation site is located in the promoter region of the FTO gene on chromosome 18 of the bovine genome, specifically, the A base at the -33 base position upstream of the transcription start site is mutated to the G base (chromosome coordinate: Chr:22040490); this mutation significantly increases the expression level of the FTO gene and significantly enhances the differentiation ability of intramuscular fat precursor cells; the FTO gene promoter mutation site provided by the present invention can not only increase the gene expression level, but also promote the differentiation of intramuscular fat precursor cells, providing a solid technical foundation for the cultivation of new beef cattle breeds and the improvement of intramuscular fat content.

The application discloses a method for eRNA transcription identification, regulation target prediction and function annotation based on high-throughput transcriptome sequencing data, and is characterized in that the method comprises the following steps: identifying part of non-coding RNA in which a transcription start site is located in an enhancer region as eRNA; obtaining eRNA-related protein coding genes which simultaneously exist in an eRNA-protein coding gene co-expression network and an eRNA-centered regulation network, constructing an eRNA-protein coding gene relationship network, and extracting protein coding genes which are directly connected or closely connected to the eRNA, so as to predict potential regulation targets of the eRNA; and finally, performing function enrichment analysis on the potential regulation targets of the eRNA, so as to obtain the results of eRNA function annotation, and the method has the advantages of wider application range, and can be applied to all eRNAs and more accurately obtain the action forms between the eRNA and the protein coding gene.

Methods and compositions are provided for using transcription start site (TSS) profiling to identify alternate promoters that yield better transcription modulation (e.g., knockdown using CRISPRi or activation using CRISPRa). Methods can also include designing CRISPR-Cas guide RNAs to target CRISPRi or CRISPRa complexes to the identified alternative promoters, and methods can also include steps of generating such guide RNAs. Also provided are libraries of guide RNA, methods of modulating expression of a target gene. In some cases, multiple promoters for the same gene are targeted simultaneously.

The present invention belongs to the field of molecular biology and discloses a variant site in the promoter region of the DGAT1 gene and its application in detecting the intramuscular fat content of pork. The SNP molecular marker is located 379bp upstream of the transcription start codon in the promoter region of the DGAT1 gene, and the base of this site is C or T. The intramuscular fat content of pork is determined according to the genotype of the mutation site. The present invention screens a SNP site related to intramuscular fat content in the promoter region, thereby obtaining a functional gene and molecular genetic marker related to intramuscular fat content. By optimizing the dominant allele of the SNP molecular marker and rapidly detecting the site, a reference basis can be provided for SNP molecular marker-assisted breeding related to the regulation of intramuscular fat content in pork, and at the same time, it has important significance for improving pork quality.

Provided herein are isolated nucleic acids, vectors, recombinant cells, and transgenic animal tremor longimanus capable of expressing at least one or more tremor longimanus genes. Also provided are recombinant cells and transgenic animals comprising one or more abrupt hair gene-specific deletions in the regulatory region upstream of the identified transcription initiation site.