Regulatory sequences nucleic acid. Medical search. Frequent questions

A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. (wikipedia.org)
Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence. (wikipedia.org)
This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. (biomedcentral.com)
Only two of the 147 genes contain a TTA codon, but some effects of bldA could be traced to TTA codons in regulatory genes or polycistronic operons. (biomedcentral.com)
We therefore generated mice carrying an affinity-tagged E2A knock-in allele to provide a system for the direct elucidation of E2A target genes based on E2A binding to target regulatory regions. (duke.edu)
FAE ( Fatty Acid Elongation ) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS ( Ketoacyl-CoA synthase ) and ELO ( Elongation Defective Elongase ) sub-gene families. (nature.com)
In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. (nature.com)
The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. (nature.com)
The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance. (nature.com)
We developed TS-REX, a database/software system that supports the analysis of tissue and cell type-specific transcription factor-gene networks based on expressed sequence tag abundance of transcription factor-encoding genes in UniGene EST libraries. (lu.se)
In order to test this hypothesis and understand the molecular basis for hsp70 expression, we compared basal hsp70 mRNA levels in males and females, and analysed the 5′ and 3′ regulatory regions of hsp70 genes in warm- and cold-climate isochromosomal O 3 + 4 + 7 and O ST lines of D. subobscura. (uab.cat)
Next, we have identified six genes that have an interaction with the regulatory regions and may be regulated by these regions. (knaw.nl)
Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)
Exploiting the aforementioned catalogs of driver genes, for example, we recently revealed the mutational landscape of chromatin regulatory factors (CRFs) in cancer [ 5 ]. (biomedcentral.com)
In spite of the importance of this tissue in the quality and production of pollen grains, studies on promoter gene regulation of tapetal expressed genes are very few and there are no reports on specific cis regulatory sequences that control tapetal gene expression. (tamu.edu)
However, to benefit from these genetic acquisitions, the bacterium must integrate the expression of these new genes into existing regulatory nodes and deploy them at the right time. (mcmaster.ca)
By identifying genes that have undergone regulatory evolution, a deeper understanding of the arms race between host and pathogen is gained. (mcmaster.ca)
Cis-acting DNA sequences which can increase transcription of genes. (bvsalud.org)
Dimerized STATs then translocate to the nucleus, where they bind DNA in the promoter sequences of target genes to activate transcription. (medscape.com)
Experiments involving the deliberate formation of synthetic or recombinant DNA containing genes for the biosynthesis of select toxins lethal for vertebrates at an LD 50 <100 ng/kg body weight (ie, nucleic acids that encode select toxins). (cdc.gov)
In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)

Therefore, to address the growing volumes of available genomic sequence, a number of algorithms that identify putative cis-regulatory modules and transcription factor binding sites using evolutionary comparisons, whole-genome data, and known descriptions of transcription factor binding sites, have been successfully developed. (biomedcentral.com)
Exploring genetic variation in the tomato ( Solanum section Lycopersicon) clade by whole-genome sequencing. (genomeweb.com)
Variant detection sensitivity and biases in whole genome and exome sequencing. (genomeweb.com)
Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds. (genomeweb.com)
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. (lu.se)

Restriction site associated DNA sequencing for tumour mutation burden estimation and mutation signature analysis. (otago.ac.nz)
The analysis of a sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. (wustl.edu)

This is reinforced by the lack of important differential features in the number and structure of regulatory elements between both arrangements, despite the genetic differentiation observed when the complete 5′ and 3′ regulatory regions were considered. (uab.cat)
Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. (genomeweb.com)
Fast and cost-effective genetic mapping in apple using next-generation sequencing. (genomeweb.com)

A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome‑wide transcriptional sequencing was performed. (spandidos-publications.com)
Specific sites within such regions are recognized by regulatory proteins (transcription factors), which act upon binding as transcriptional repressors or activators, controlling the rate of transcription. (biomedcentral.com)

RSAT 2018: regulatory sequence analysis tools 20th anniversary. (nih.gov)

The potential application of our method includes annotation of new genomic sequences and motif discovery. (biomedcentral.com)
The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. (lu.se)

Originally discovered as a chief regulatory protein of glucose and lipid metabolism and cell differentiation, the peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-activated transcription factor of the nuclear hormone receptor superfamily 8 . (nature.com)
These recruitment events are inhibited in a normal wild type HSV-1 infection by the viral regulatory protein ICP0. (mdpi.com)
This was gradually expanded into various methods in bioinformatics, in particular for sequence analysis and protein structure prediction. (ntnu.edu)
EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive approximately 60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. (uky.edu)

We employed conditional translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines expressing human PARIS wild type (WT) or mutant (C571A). (nature.com)

Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. (genomeweb.com)

Among this constellation of sequences, enhancers and their associated transcription factor proteins have a leading role in the regulation of gene expression. (wikipedia.org)
Comparatively short sequences (several hundred to several thousand base pairs, depending on thespecies) upstream or downstream of the transcription start site often play a major role in the regulation of gene expression. (biomedcentral.com)
A cis regulatory element in the TAPNAC promoter directs tapetal gene expression. (tamu.edu)

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. (psu.edu)

We observed that single nucleotide polymorphisms (SNPs) residing within nearby regulatory regions show significant polygenicity and contribute between 59-71% of the heritability for MI/CAD. (nih.gov)
Regulatory regions of higher eukaryotes can be subdivided into proximal regulatory units - promoters - which are located close to and upstream of the gene, and distal transcription regulatory units called enhancers or cis-regulatory modules. (biomedcentral.com)
Recognition of regulatory DNA regions based on description of known transcription factor binding sites (TFBS). (biomedcentral.com)
Extracting clustered recognition motifs is one of the most reliable techniques, but is limited to the recognition of similarly regulated cis-regulatory regions. (biomedcentral.com)
Methods of this type assume that regulatory regions are highly conserved in cross-genomic comparison, and conserved segments can be extracted from evolutionary related genomes. (biomedcentral.com)
Furthermore, it is still an open question as to how many genomes are sufficient for reliable extraction of regulatory regions. (biomedcentral.com)
In A6 cells, Runx2 was found to modulate MGP transcription and deletion analysis of MGP distal and proximal promoter-luciferase constructs identified cis-regulatory regions. (bath.ac.uk)
Low levels of E2A binding were observed at several other lymphoid-restricted regulatory regions including the Ig heavy chain (IgH) intronic enhancer, the IgH 3' enhancers hs3b/hs4, the RAG-2 enhancer, and the 5' regions of the B29 and TdT loci. (duke.edu)
Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions. (psu.edu)
We identify a mutagenic effect of active demethylation primarily acting in regulatory regions and a mutagenic effect of long interspersed nuclear elements. (wustl.edu)
We have focused on these regulatory regions and discovered that the DNA that is linked to intracranial aneurysms often overlaps with such regulatory DNA regions. (knaw.nl)
Lastly, we have tested whether these regulatory DNA regions can really regulate gene activity and found that most of them can. (knaw.nl)
4462 functional sequence variations in regulatory DNA regions in training dataset F1 and 1116 functional SNVs in test datasets F2. (lu.se)

This is an actively progressing area, as more and more sequenced genomes appear. (biomedcentral.com)

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. (genomeweb.com)

The many biochemical reactions catalyzed by PLP-dependent enzymes are involved in essential biological processes, such as hemoglobin and amino acid biosynthesis, as well as fatty acid metabolism . (oregonstate.edu)
Other neurotransmitters, including glycine, D-serine, glutamate, histamine, and γ-aminobutyric acid (GABA), are also synthesized in reactions catalyzed by PLP-dependent enzymes (7) . (oregonstate.edu)
Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer. (genomeweb.com)

The research group has established rigorous methods for benchmarking methods for motif discovery (BMC Bioinformatics 2007, 2008) and ChIP-seq data analysis (Nucleic Acids Res 2011). (ntnu.edu)

Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to control mRNA biogenesis or translation. (wikipedia.org)

PLP is also a coenzyme for reactions that generate glucose from amino acids, a process known as gluconeogenesis (6) . (oregonstate.edu)
Roles of neuroactive amino acids in ammonia neurotoxicity. (cdc.gov)

Mediator (coactivator) (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to the RNA polymerase II (RNAP II) enzyme bound to the promoter. (wikipedia.org)
The TAPNAC promoter was studied in detail to identify cis regulatory sequences that confer tapetal specific expression. (tamu.edu)
Mendelian regulatory variations including 42 enhancer, 142 promoter, 153 5' UTR, 43 3' UTR, 65 RNA gene, 3 imprinting control region, and 5 microRNA gene variations. (lu.se)

Abelson-transformed pre-B cell lines derived from these mice were used in chromatin immunoprecipitation experiments to identify regulatory sequences bound by E2A in the context of an early B lymphocyte environment. (duke.edu)

2014. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation . (umd.edu)

Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. (nature.com)
Fatty acids of this group can be found abundantly in the form of suberins, sphingolipids, leaf cuticles, pollen epidermis, and cork cells. (nature.com)

Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. (biomedcentral.com)

225 Functional regulatory SNVs in monogenic and complex diseases and 241910 SNVs from dbSNP as a negative control dataset. (lu.se)

With the development of next-generation sequencing (NGS), research has focused on comprehensive genomic analysis based on tumor molecular features, such as somatic mutations and copy number variation. (spandidos-publications.com)
Nucleic Acids Research, 45(5), 2307-2317. (lu.se)
DSAT continues to encourage entities to practice due diligence and request a review of research that could potentially meet the regulatory definition of a restricted experiment out of an abundance of caution to protect public health and safety and prevent any potential compliance action. (cdc.gov)

It is accomplished through the sequence-specific binding of proteins (transcription factors) that activate or inhibit transcription. (wikipedia.org)

Click molecule labels to explore molecular sequence information. (nih.gov)

To build a foundation necessary to engineer robust ethanol-producing cyanobacterial hosts, in this study we applied a quantitative transcriptomics approach with a next-generation sequencing technology, combined with quantitative reverse-transcript PCR (RT-PCR) analysis, to reveal the global metabolic responses to ethanol in model cyanobacterial Synechocystis sp. (biomedcentral.com)

Prediction of functional regulatory SNPs in monogenic and complex disease. (lu.se)

Genome sequencing of normal cells reveals developmental lineages and mutational processes. (genomeweb.com)

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. (genomeweb.com)
27558 Mendelian disease regulatory variants from OMIM and ClinVar, 20963 complex disease regulatory variants from VarDi and NHGRI GWAS Catalog and 43364 recurrent cancer somatic variations. (lu.se)
Disease-associated variants in different categories of disease located in distinct regulatory elements. (lu.se)
Quantifying deleterious effects of regulatory variants. (lu.se)

Currently, there are three basic types of tests to determine if an individual has been infected with SARS-CoV-2: viral nucleic acid (RNA) detection, viral antigen detection, and detection of antibodies to the virus. (medscape.com)
Viral tests (nucleic acid or antigen detection tests) are used to assess acute infection, whereas antibody tests provide evidence of prior infection with SARS-CoV-2. (medscape.com)
Wooden shafts or calcium alginate swabs may contain substances that inhibit some viruses and nucleic acid detection reactions. (medscape.com)

A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. (uky.edu)

Cis-regulatory programs in the development and evolution of vertebrate paired appendages. (uchicago.edu)

Unlocking the secondary gene-pool of barley with next-generation sequencing. (genomeweb.com)
Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology. (genomeweb.com)

A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa‑miR‑940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa‑miR‑940/cingulin‑like 1 (CGNL1). (spandidos-publications.com)
To address the mechanism of isoform-specific mRNA localization, molecular chimeras were constructed by insertion of actin sequences between the Lac Z coding region and SV-40 3'UTR in a reporter plasmid. (umassmed.edu)

These cis-regulatory sequences include enhancers, silencers, insulators and tethering elements. (wikipedia.org)
Enhancers are sequences of the genome that are major gene-regulatory elements. (wikipedia.org)

Currently, 3 types of experiments meet the regulatory definition of a restricted experiment (42 CFR 73.13). (cdc.gov)
Experiments involving the creation of SARS-CoV/SARS-CoV-2 chimeric viruses resulting from any deliberate manipulation of SARS-CoV-2 to incorporate nucleic acids coding for SARS-CoV virulence factors or vice versa. (cdc.gov)

Notably, these results were consistent with those obtained using high‑throughput sequencing. (spandidos-publications.com)
Assessing the impact of water treatment on bacterial biofilms in drinking water distribution systems using high-throughput DNA sequencing. (genomeweb.com)

We localize a mutagenic process specific to oocytes from population sequencing data. (wustl.edu)
In contrast, sequences from the 5'UTR through the coding region of either actin gene did not localize the blue product. (umassmed.edu)

Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data. (otago.ac.nz)
We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. (biomedcentral.com)

Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. (psu.edu)

Beyond the regulatory elements, the only notable difference between both arrangements is the presence in 3′ UTR of a 14 bp additional fragment after the stop codon in the hsp70A copy in five O 3 + 4 + 7 lines, which was not found in any of the six O ST lines. (uab.cat)

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