47 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 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 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.

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 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.

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 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.

A method for increasing gene expression and improving herbicide resistance in plants. Specifically, the method involves performing modifications at upstream and downstream regions of a transcription start site of a gene of interest by means of a genome editing technique, so as to modify a non-coding region of the gene, thereby increasing the expression level of an endogenous polynucleotide or the gene of interest. Furthermore, the method is used to modify and regulate an HPPD gene and / or HIS1 gene associated with herbicide resistance in the plants, thereby improving herbicide resistance in the plants.

The invention relates to the field of gene engineering, in particular to a plasmid elimination module based on an inducible promoter, which comprises two types of mutually independent expression regions, one type of region is an inducible factor transcription region, and the inducible factor transcription region is composed of a constitutive promoter carried by an inducible transcription factor fragment, and the other type of region is an inducible transcription factor fragment. The kit comprises an RNA polymerase binding site, a transcription start site, a ribosome binding site, an induced transcription factor translation region and a terminator, the other region is an antisense RNA expression region and comprises an inducible factor promoter corresponding to an inducible transcription factor, an antisense RNA and a terminator; the antisense RNA is the antisense RNA of the 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 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 discloses an SNP (Single Nucleotide Polymorphism) molecular marker related to a pig body length character and application of the SNP molecular marker, and belongs to the technical field of biology. The SNP molecular marker is as follows: rs696067660Cgt; t is located on a No.15 chromosome of a pig, and the SNP site is located in a pig GALNT13 gene promoter region (the transcription start site is + 1, and the upstream-678th base site). The SNP molecular marker related to the pig body length character is disclosed for the first time, is used for distinguishing individuals with medium and short body lengths and individuals with long body lengths, is suitable for domestic pig breeds and foreign pig breeds, and is wide in pig breed application range. The method for detecting the genotype of the SNP molecular marker disclosed by the invention can be used for quickly and effectively predicting the body length of a pig in an early stage at low cost, has a wide application prospect in the aspect of improvement of a pig variety strain, and can obtain an excellent economic value.

The present invention discloses a method for predicting key transcription factors based on enhancer and promoter data, which comprises the following steps: obtaining a FASTA format file of a gene enhancer sequence; obtaining a FASTA format file of a gene promoter sequence based on the positional information of the gene transcription start site; importing the FASTA format files of the gene enhancer sequence and the promoter sequence into the transcription factor online prediction system PROMO respectively, to obtain a transcription factor that targets the enhancer and a transcription factor that targets the promoter; screening out integrated transcription factors that simultaneously target the enhancer and the promoter; constructing a protein interaction network of the integrated transcription factors; screening transcription factors in core positions as key transcription factors that regulate gene expression. The present invention can accurately and quickly predict key transcription factors that regulate gene expression by integrating enhancer and promoter data, and has higher prediction accuracy.

The present invention relates to synthetic enhancer elements that can be used to increase the expression of a gene of interest in any plant tissue. The disclosed synthetic enhancer elements can be used in a gene expression cassette comprising nucleic acid further comprising a promoter and a sequence to be expressed, wherein the sequence to be expressed has a transcription start site, and wherein the synthetic enhancer element is operably linked to the promoter and the sequence to be expressed. The present invention also relates to a modified plant or part thereof comprising a synthetic enhancer element, wherein the synthetic enhancer element is operably linked to an endogenous promoter in the modified plant or part thereof and an endogenous gene in the modified plant or part thereof, and wherein the synthetic enhancer element increases expression of a transcript or protein encoded by the endogenous gene.

The application belongs to the field of molecular biology, and discloses a SNP molecular marker related to a pig backfat thickness character and application thereof. The application screens a SNP site g.348A>G related to the pig backfat thickness character in an intron region of an ADIPOQ gene. The SNP site is located at a 348bp nucleotide downstream of a transcription start site of the ADIPOQ gene, and the polymorphism is A or G. The genotype of the mutation site is used to determine the pig backfat thickness, thereby obtaining a functional gene and a molecular genetic marker related to the pig backfat thickness. Through selection of a dominant allele of the SNP molecular marker and rapid detection of the site, a reference basis can be provided for accurate evaluation of a pig fat deposition capacity regulation related SNP molecular marker assisted breeding, and the application has important significance for pig line or breed improvement.

The invention discloses an efficient new transcript 5'end library building method. According to the present invention, the new RNA transcription start site sequencing technology (NSS-seq) is developed, and the new RNA purification of the RNA-DNA-RNAII compound and the optimized template strand displacement are combined so as to be used for the 5'end capture of the new RNA; the NSS-seq obviously reduces the initial cell quantity required by the experiment, and the research can be carried out even if the biological material is limited. Meanwhile, the experiment method is simplified, so that the experiment can be completed in a standard molecular laboratory within one day. Therefore, the NSS-seq provides a more efficient experimental scheme for the research of the transcription start site of the new transcript.

The present invention relates to a compound of formula (I) or pharmaceutically acceptable salts, stereoisomers, diastereoisomers, enantiomers, polymorphs, racemic mixtures, solvates or isomers and mixtures thereof. The invention also relates to a process for the stereoselective preparation of such compounds. The compounds of formula (I) are useful as medicaments, in particular for inhibiting crown protein 1 expression in the induction of immunosuppression or in the treatment and / or prevention of diseases or disorders selected from the group consisting of transplant rejection, autoimmune diseases, inflammatory diseases, infectious diseases and lymphoproliferative disorders. The present invention also relates to a vector comprising a crown protein 1 promoter element wherein the crown protein 1 promoter element starts directly upstream of the transcription start site (TSS) of the crown protein 1 gene and spans a sequence segment of at least about 700 bp in the genome in the vertebrate genome. The invention also relates to a method for identifying immunomodulatory compounds that alter the activity of the crown protein 1 promoter using said vector. The invention also relates to BRD3 as an upstream target responsible for driving crown protein-1 expression and activity in immune cells, and to compounds that selectively target the bromodomain of BRD3 and thereby deplete crown protein 1 levels, in particular compounds of formula (I). # imgabs0 #