Position weight sequence regulatory elements transcriptional. Medical search. Frequent questions

The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. (biomedcentral.com)
Transcriptional regulation is modulated by a complex network of interactions between regulatory proteins and their binding targets on DNA. (biomedcentral.com)
The graphic display of an operon contains all the genes of its different transcription units, as well as all the regulatory elements involved in the transcription and regulation of those TUs. (wikipedia.org)
Hannenhalli's current research focuses on comparative genomics, transcriptional regulation, and evolution. (umd.edu)
Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. (biomedcentral.com)
Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. (biomedcentral.com)
Notably, a large number of stress-related elements present in the promoter regions of some ZmCAMTA genes, indicating a genetic basis of stress expression regulation of these genes. (frontiersin.org)
CAMTAs participate in gene expression regulation by binding to the cis -elements in the promoter regions of numerous target genes. (frontiersin.org)
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. (omicsdi.org)
Our ultimate goal is to create a complete, quantitative model of photoreceptor transcriptional regulation including a detailed cis -regulatory grammar. (wustl.edu)
MicroRNAs are a class of endogenous, small non-coding RNAs (20-24 nucleotides) with critical roles in the post-transcriptional regulation of gene expression [ 1 ]. (biomedcentral.com)
MicroRNAs (miRNAs) are an abundant class of small (approximately 22 nt) endogenous non-coding RNAs that direct post-transcriptional regulation of gene expression. (biomedcentral.com)
Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)

Recent studies have found that non-coding RNAs and post transcriptional modification of RNAs have become the active fields of cancer research. (biomedcentral.com)

The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. (expasy.org)
Finally, CcpA controls a complex and extended regulatory network through the modulation of a large set of regulators. (studyres.com)
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. (biomedcentral.com)

A database of in vitro selected TFBS sequences obtained with high-throughput SELEX. (expasy.org)
The HTPSELEX database contains sets of in vitro selected transcription factor binding site sequences obtained with the high-throughput SELEX (HTPSELEX) method. (expasy.org)
Our approach is to cluster genomic positions into groups exhibiting distinct "fingerprints" based on high-throughput functional genomic data, then to estimate a probability of fitness consequences for each group from associated patterns of genetic polymorphism and divergence. (biorxiv.org)
Different studies based on computational analysis on both expressed sequence tags and high-throughput RNA sequencing provide an estimate of the frequency of these events. (biomedcentral.com)
Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced [ 12 ]. (biomedcentral.com)
Here, we used ChIP followed by high-throughput sequencing (ChIP-seq) to analyse genomic occupancy of CFP1 in two human haematopoietic cell types. (biomedcentral.com)

A promoter is defined in RegulonDB as the nucleotide sequence 60 bases upstream and 20 downstream from the precise initiation of transcription or +1. (wikipedia.org)
30 bps) and have a typical nucleotide sequence, although there may normally be variations due to mutations that occurred because of the selective pressure that the genome has undergone over time [ 4 ]. (biomedcentral.com)
It is also called nucleotide sequence. (lookformedical.com)

Many computational methods for gaining functional insights from sequence data are based on the simple, but powerful, observation that functionally important nucleotides tend to remain unchanged over evolutionary time, because mutations at these sites generally reduce fitness and are therefore eliminated by natural selection 7 - 15 . (biorxiv.org)

In bacteria, such as E. coli, genes, are regulated by sequence elements in promoters and related binding sites). (wikipedia.org)
It also hosts a large collection of so-called derived data such as ChIP-seq peaks, genome annotations (e.g. promoters, splice-junctions, etc.), and sequence-intrinsic data (conservation scores, SNPs, indel, etc. (expasy.org)
We analyzed respective gene promoters' sequences using in silico methods for identification of transcription binding sites, mainly in the NF-κB- and IRF-coding genes. (biomedcentral.com)
An analysis of cis-regulatory elements indicated that bZIP promoters were associated with phytohormones and stress responses. (biomedcentral.com)
Indeed, in the absence of PRDM9, meiotic DSBs occur at transcription regulatory regions, such as promoters and enhancers (Brick et al. (springer.com)

SSA is a software package and a Web interface for the analysis of sequence motifs that occur at constrained distances from functional sites, such as transcription initiation sites or transcription factor binding sites. (expasy.org)
We have developed an approach for detecting motifs in biopolymers sequences. (biomedcentral.com)
Sequence motifs are small sequences capable of acting as binding sites for a particular transcription factor [ 1 ]. (biomedcentral.com)
Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific RBP binding motifs. (biomedcentral.com)
Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. (biomedcentral.com)

It involves crosslinking cells to lock RNA-protein interactions, immunoprecipitating the complexes using an antibody specifically targeted to the RBP, sequencing cDNA reverse transcribed from the captured RNA, and statistically analyzing the aligned sequencing reads [ 26 ]. (biomedcentral.com)
However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)

The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). (omicsdi.org)

With the exception of late blight resistance, the other novel traits (i.e. reduced asparagine levels, lower levels of reducing sugars, and reduced black spot bruising) are achieved through the transcription of inverted repeat sequences containing small fragments of DNA from five different endogenous genes (i.e. (canada.ca)
the invention also provides non-human animals and cells comprising a transgene encoding an APP comprising the Swedish mutation and further comprising functionally disrupted endogenous APP gene loci, transgenes and targeting constructs used to produce such transgenic cells and animals, transgenes encoding human Swedish mutation APP polypeptide sequences, and methods for using the transgenic animals in pharmaceutical screening and as commercial research animals for modeling neurodegenerative diseases (e.g. (justia.com)
We describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. (cdc.gov)

The transcriptome analyser (TROMER) project provides tools to determine and document all the transcribed elements of a genome. (expasy.org)

We then surveyed the distribution of stress-related cis -regulatory elements in the −1.5 kb promoter regions of ZmCAMTA genes. (frontiersin.org)

TagScan allows searching for perfect matches and for single or double nucleotide mismatches between oligonucleotide queries of up to 60 bases and sequence databases comprising entire genomes or mRNA reference sequences. (expasy.org)

While many CTCF binding sites fall within transposable elements (TEs), their contribution to 3D chromatin structural evolution is unknown. (nature.com)
While some TE-derived CTCF-binding sites may cause deleterious effects and be eliminated from the population, others may be maintained in the population as selectively neutral variants that may later be exapted for regulatory purposes, including chromatin loop anchoring. (nature.com)
Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. (omicsdi.org)
iii) FOXA factors are associated with sex-dependent chromatin opening at male-biased but not female-biased regulatory sites. (omicsdi.org)
v) The male-biased repressor BCL6 preferentially targets female-biased genes and regulatory sites in a sex-independent chromatin state. (omicsdi.org)
Journal Article Genome Res · June 2021 Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. (duke.edu)
Journal Article · June 29, 2020 AbstractThough the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. (duke.edu)
Recently, they generated comprehensive maps of rod- and cone-specific open chromatin using ATAC-seq and have leveraged these maps to elucidate the differences in cis -regulatory grammar between these two cell types. (wustl.edu)
One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
Using combination of chromatin immunoprecipitation and genome sequence analysis, we detected 55 CcpA binding sites corresponding to 140 genes directly controlled by CcpA. (studyres.com)
These regions are known as CpG islands (CGIs) and consist of short (~ 1000 bp) interspersed CpG-rich and predominantly unmethylated DNA sequences [ 1 ], which are associated with transcriptionally permissive chromatin state [ 2 ]. (biomedcentral.com)

RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. (wikipedia.org)
RegulonDB provides a database of such regulatory elements, their binding sites and the transcription factors that bind to these sites in E. coli. (wikipedia.org)
this represents a recovery of 52% of the 1592 annotated regulatory interactions in the database for the 93 TFs for which RegulonDB has a position-weight matrix (PWM). (wikipedia.org)

FIGS. 8A-C depict amino acid sequences of wild-type and variant AAV capsids. (justia.com)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

The complete repertoire of 189 genetic sensory-response units (GENSOR units) are reported, integrating their signal, regulatory interactions, and metabolic pathways. (wikipedia.org)

Around half of these elements are located within intergenic regions (2'139) and the rest are located within non-coding parts of genes: introns (1'713) and UTRs 499). (expasy.org)
Recent research has revisited the topic of TE impact on gene expression, noting that the dissemination of highly similar sequence accomplished by TEs is a powerful way to link many diverse genomic regions into a regulatory network [ 7 ]. (biomedcentral.com)
The first step in this process is the identification of regions of the genome that contain regulatory information. (sdbonline.org)
Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
This is particularly important at regulatory regions, such as CpG islands (CGIs), which are known to recruit Trithorax (TrxG) and Polycomb group proteins. (biomedcentral.com)

Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. (biomedcentral.com)
Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. (biomedcentral.com)

A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. (biomedcentral.com)
While highly effective in some cases, a potential drawback of this approach is that the process of isolating a subgroup of sequences, typically done using clustering, cutoffs, or functional categorization, can be arbitrary. (biomedcentral.com)
During the past decade, two major developments-the emergence of massively parallel, ultra-cheap DNA sequencing technologies and the use of these technologies as digital readouts for functional genomic assays-have led to a profusion of data describing various features of genomes, epigenomes, and transcriptomes 1 , 2 . (biorxiv.org)
These conservation-based methods, however, depend critically on the assumption that genomic elements are present at orthologous locations and maintain similar functional roles over relatively long evolutionary time periods. (biorxiv.org)
Evolutionary turnover may cause inconsistencies between sequence orthology and functional homology that substantially limit this type of analysis. (biorxiv.org)
This important limitation has led to two major alternative strategies for the identification and characterization of functional elements. (biorxiv.org)
High-molecular-weight insoluble polymers that contain functional cationic groups capable of undergoing exchange reactions with anions. (lookformedical.com)

In higher eukaryotes, this cis-regulatory information is organized into modular units [cis-regulatory modules (CRMs)] of a few hundred base pairs. (sdbonline.org)
Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. (lookformedical.com)

A method for determining the sequence specificity of DNA-binding proteins. (lookformedical.com)

The ChIP-Seq Web Server is a comprehensive online resource for analysing ChIP-Seq data and other types of mass genome annotation data RNA-seq, DNA-methylation and sequence-derived features). (expasy.org)
MSeq which is a software pipeline used to derive TFBS models from DNA sequences such as HT-SELEX and MITOMI-seq, PWMEval and PWMScore that are tools used to evaluate PWM models based on ChIP-seq data, and PWMScan which is a tool to scan entire genomes of common model organisms with a PWM. (expasy.org)
MFMD performance was assessed using ChIP-seq data retrieved from the JASPAR site, promoter sequences extracted from the ABS site, and artificially generated synthetic data. (biomedcentral.com)

An operon is here conceived as a structural unit encompassing all genes and regulatory elements. (wikipedia.org)

We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. (biomedcentral.com)
The non-structural rep gene encodes four regulatory proteins essential for viral replication, whereas cap encodes three structural proteins (VP1-3) that assemble into a 60-mer capsid shell. (justia.com)
Comparative analysis of these pathways relies on network alignment methods, much the same way as sequence matching and alignments are used for individual genes and proteins. (biomedcentral.com)

miRNAs are either expressed from independent transcriptional units or derive from introns of protein-coding genes or exons or introns of long ncRNAs. (biomedcentral.com)

A TU may also include regulatory protein binding sites affecting this promoter and a terminator. (wikipedia.org)
Stimulation of TLRs (Toll-Like Receptors) by a pathogen induces activation of signal transduction cascades, which leads to translocation of nuclear factor-κB (NF-κB) to the nucleus [ 1 ], activation of interferon regulatory factors 3/7 (IRF3/7) and/or activator protein-1 (AP-1), which cooperate to induce transcription of various cytokines such as alpha/beta interferon (IFN-α/β) to counteract infection [ 2 - 4 ]. (biomedcentral.com)
Protein sequence analysis showed BmLP7, similar to reported lipoprotein-3 (BmLP3), contains the cell-penetrating peptides and Cysteine position, while BmLP1 has not. (bvsalud.org)
This study provides evidence that a switch-protein kinase regulatory network controls availability of σ 66 , the main sigma subunit for transcription in Chlamydia . (plos.org)
Accepted August 23, 2012 ABSTRACT The catabolite control protein CcpA is a pleiotropic regulator that mediates the global transcriptional response to rapidly catabolizable carbohydrates, like glucose in Gram-positive bacteria. (studyres.com)
E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)

Exact approaches usually use the consensus sequence for motif representation, employing some mathematical optimization as the search model. (biomedcentral.com)

Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. (biomedcentral.com)
Correspondence with low molecular weight chemicals that results in the priming of chemical-specific, Prof. Dr. Stefan F. Martin, Allergy Research skin-homing CD8+ Tc1/Tc17 and CD4+ Th1/Th17 cells. (cdc.gov)

Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. (biomedcentral.com)
A cis-regulatory element (CRE) analysis suggested that the euAP2 s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. (biomedcentral.com)

In a number of cases, extant TE sequences have integrated with established genomic functions and been co-opted by the genome for critical roles [ 7 ],[ 8 ]. (biomedcentral.com)
Estrogen-related receptors (ERRs) are transcriptional regulatory factors that play crucial roles in mammalian energy storage and expenditure. (bvsalud.org)

A common strategy among computational tools developed for this purpose is to first obtain a small group of genes in which a given motif may be statistically over-represented, from which the motif can then be elicited using methods such as position weight matrix updating and word enumeration [ 6 - 10 ]. (biomedcentral.com)
Position Weight Matrix model generation and evaluation tools. (expasy.org)
PWMTools is a Web interface for Position Weight Matrix (PWM) model generation and evaluation. (expasy.org)
Probabilistic methods try to maximize the relative entropy or Kullback-Leibler divergence [ 7 ], obtained from the construction of a Position Specific Score Matrix (PSSM). (biomedcentral.com)

REDUCE is a deterministic method that first enumerates oligonucleotides and then identifies words whose occurrence in promoter sequences correlate most strongly with expression data. (biomedcentral.com)

To maximize the number of core genome sites available for SNP comparison, core genome SNP-based analyses were repeated by using a draft assembled genome of 1 representative clinical strain (isolate B2) as a reference sequence. (cdc.gov)
Our curation knowledge is currently mapped to the GenBank Reference Sequence for E. coli K12. (unam.mx)

Oct. 26, 1993, Abstract No. 15.4, Anaheim, Calif.) which contains more of the .beta.AP sequence carboxy terminal to that form described by Esch et al. (justia.com)

By the way, it's alone because they're jealous, depressed, and weak-minded [url=http://aafscny.org/programs/event3/item2/]purchase 60mg orlistat amex[/url] weight loss pills similar to adderall. (wgc2010.sk)

For example, the algorithm REDUCE (Regulatory Element Detection Using Correlation with Expression) avoids subgroup selection in a natural way by genome-wide fitting of motif counts to expression data [ 15 ]. (biomedcentral.com)
Clustering tool for one-dimensional genome annotation data mapped onto genome sequences. (expasy.org)
We have generated fitCons scores for three human cell types based on public data from EN-CODE. (biorxiv.org)

We describe a novel computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. (biorxiv.org)
the extent to which they do can be used as the basis for the computational identification of cis-regulatory modules. (sdbonline.org)

To potentiate the use of high- quality SNPs, only variant calls passing default criteria ( 5 ) were considered in the Harvest approach, while for Snippy, only variant sites with minimum mapping quality of 60, minimum number of reads covering the variant position of 10, and minimum proportion of reads differing from the reference of 90% were considered for downstream analysis. (cdc.gov)
A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3′ coding region. (biomedcentral.com)
This averaging effect hampered the analysis of finer regulatory mechanisms at the single-cell level, the fundamental unit for any fate decision process. (lu.se)

Raw sequence reads of the 25 C. difficile isolates subjected to WGS were deposited in Sequence Read Archive under the accession nos. (cdc.gov)

In addition, if an enzyme is used in signal transduction, fixed-length DNA sequences may produce unexpected results.To solve these problems, this paper proposes a recognition molecule DNA sequence generation algorithm that reflects the properties of DNA and allows stable hybridization, when DNA is used for molecule recognition in the bioreceptor. (agckinases.com)
The proposed bioreceptor recognition molecule DNA sequence generation algorithm applies an evolution algorithm for the generation of the initial recognition molecule DNA sequences. (agckinases.com)
As shown in Figure 1, the structure of the recognition molecule DNA sequence algorithm is an enhancement of Adleman��s DNA computing algorithm. (agckinases.com)
It is comprised of a pre and post-process and takes into account the characteristics and capabilities of using TSP in the approach.Figure 1.The flow of the recognition molecule receptor DNA sequence generation algorithm.First, the preprocess layer is divided into the encoding, initialization and fitness evaluation methods. (agckinases.com)
The encoding method generates variable-length edges, including vertexes and weights, using the evolution algorithm, in order for the given sequence to reflect the characteristics of DNA molecules. (agckinases.com)

2011) modelled the plant biomass (dry weight) in wheat ( Triticum aestivum L.) as a linear function of projected area, assuming plant density was constant. (biorxiv.org)

Hold Mechanism of Medicines of Latvia is constant a community media rivalry between 7-11 November 2016 to recommend reporting of suspected medicines side effects, as element of an EU-wide awareness week. (wgc2010.sk)

amyloid peptide sequence (Esch et al. (justia.com)

We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)

In our previous work, we identified the metadata elements that are crucial to the description of Web APIs and subsequently developed the smartAPI metadata specification using the FAIR (Findable, Accessible, Interoperable, Reusable) principles. (stanford.edu)

Compared with conventional conservation scores, fitCons scores show considerably improved prediction power for cis -regulatory elements. (biorxiv.org)

The regulatory mechanisms of activation of these two pathways and their interactions during the IIR are only partially known. (biomedcentral.com)
Tiling a given promoter region with several sgRNAs can produce more robust transcriptional activation 9 - 11 , but this requirement presents enormous challenges for scalability, and in particular for establishing pooled, genome-wide GOF screens. (cdc.gov)

A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)

The vertexes and edges cannot be expressed directly, and they are converted to DNA sequences using the procedure illustrated in Figure 2. (agckinases.com)

Semi-automatic curation produced a total of 3,195 regulatory interactions for 199 TFs. (wikipedia.org)

This allows more stable expression of the DNA than existing fixed-length receptor DNA sequence generation, and accurately reflects the characteristics of the DNA. (agckinases.com)

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