Regulatory genes and genetic transcription factors transcription genetic. Medical search. Frequent questions

In the classical view, the steady states of a dynamical system modeling the genes, mRNAs, and proteins in this network are identified with the above two types of states. (aps.org)
In chapter 2, by using CRISPR/Cas9 gene editing, genetic analysis and biochemical assays, I identified the differential pairings of typical NLR receptor SOC3 with atypical NLR proteins CHS1 or TN2 to guard the homeostasis of the E3 ligase SAUL1. (ubc.ca)
We will use omic technologies to analyze a large variety of strains of each of the pathogens to identify genes and proteins necessary for pathogens to survive stresses encountered in food environments and cause human illness. (usda.gov)
Transcription factors like c-MYC and AP4 act as regulatory switches that enable the genetic information encoded in specific segments of the DNA to be transcribed into messenger RNA, which programs the synthesis of the corresponding proteins. (medicalxpress.com)
Signals from the environment or from other cells activate proteins called transcription factors. (medlineplus.gov)
These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription. (medlineplus.gov)
The order of nucleotides in the DNA was hypothesized and confirmed to instruct the sequence of amino acids in proteins via a temporary ('messenger') RNA copy of the gene and adaptor 'transfer RNAs' that connected the two. (taylorfrancis.com)
Although the concept of 'genetic programming' was emerging, the conclusion that genetic information is transacted primarily by proteins became entrenched, a reflection of the mechanical zeitgeist of the age, and assumed to be true both for bacteria and developmentally complex plants and animals. (taylorfrancis.com)
Gene expression studies provide us with a selection of candidate transcription factors and other regulatory proteins that are related to such memory functions. (mpg.de)
In addition, we use genetic approaches such as RNA interference, overexpression or GFP tagging to study the function and localization of the proteins in planta . (mpg.de)
2) Proteins regulated via additional regulators, including proteins involved in NNR and NarR regulons: nitrate reductase beta-subunit, TonB-dependent receptors, nitrite reductase, a TenA-type transcription regulator, and an unknown protein with an alpha/beta hydrolase fold. (nih.gov)
The functional part of the genome can be roughly broken down into two components: the coding regions, or the actual bit of DNA that is transcribed and translated into working proteins, and the subset of the non-coding regions that are involved in regulating gene expression. (freethoughtblogs.com)
dCas9 can be fused to protein tags or the effector domains of transcription factors (proteins that bind DNA in promoter regions and simultaneously bind other regulatory proteins via effector domains, which can activate or repress transcription and thereby affect gene expression) to develop customized DNA binding proteins. (jax.org)
The core transcription machinery of RNA polymerase copies the information found in DNA genes onto messenger RNA molecules that then govern the production of proteins. (sciencedaily.com)
We thought that only one set of "general" proteins was involved, and that all the regulation was directed by enhancer-binding proteins that were specific to a particular gene sequence. (sciencedaily.com)
Toll is a gene in fruit fly and toll-like proteins which was discovered in animals and also was named as TLRs. (hindawi.com)
However, for medical or environmental applications, the recombinases could be re-engineered to respond to other conditions such as acidity or the presence of specific transcription factors (proteins that control gene expression). (sciencedaily.com)
The researchers tested this approach with three genes that code for different fluorescent proteins -- green, red, and blue, constructing a circuit that expressed a different combination of the fluorescent proteins for each identity and order of two inputs. (sciencedaily.com)
Now a large and ever increasing number of genetic subtypes has been described, and major advances in molecular and cellular biology have clarified the understanding of the role of different proteins in the physiology of peripheral nerve conduction in health and in disease. (medscape.com)
Gene expression generally produces proteins, but there are also non-coding genes that produce RNA molecules (rRNA, tRNA). (lu.se)
Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)
The protein structure that surrounds the DNA, chromatin, largely comprises histone proteins and can be open or closed and thus allow or prevent factors binding to the DNA. (lu.se)
It is not only the genes that code for proteins that are methylated, but also parts of the DNA that code for regulatory functions (RNA molecules), which can have a greater effect than genes. (lu.se)

This rewiring is defined by the change in regulatory-target gene interactions, while there is still conservation of regulatory factors and target genes. (wikipedia.org)
Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. (escholarship.org)
Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. (escholarship.org)
The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. (kb.se)
Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes. (lu.se)
Exons 1-6 of the WT1 gene encode the regulatory domain, which regulates expression of target genes, and exons 7-10 encode the 4 zinc fingers of the DNA-binding region of the WT1 protein. (medscape.com)

In a population of genetically diverse individuals, the extent of genetic variation of a phenotype measures the overall sensitivity of individuals to mutations segregating in the population. (nature.com)
Like the Butterfly effect, these somatic mutations lead to a series of regulatory function changes, including gene expression dysregulation. (hep.com.cn)
hypothesized that associations between gene expression and somatic mutations can be translated into the associations between gene expression and mutational signatures for showing the regulation effects between somatic mutation and gene expression dysregulation. (hep.com.cn)
This work reveals the key message that some somatic mutations can lead to gene expression alteration consequences. (hep.com.cn)
Emergence of LSC is dependent on individual or combined genetic mutations that broadly determine the cellular affiliation of the leukemia, and permit or impose ectopic self-renewal and a restricted differentiation potential into what constitutes the proliferative bulk of the leukemia ( 5 , 6 ). (frontiersin.org)
The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. (biomedcentral.com)
Loss-of-function (LOF) mutations, including stop-gain, splice-site, and frameshift mutations, play a key role in the etiology of genetic disorders (Fig. 1 a). (biomedcentral.com)
While it is relatively straightforward to identify LOF mutations in protein-coding genes, it is challenging to infer their effects on evolutionary fitness and disease risk. (biomedcentral.com)
Introduction to loss of function (LOF) mutations, essential genes versus nonessential genes as well as LOF intolerance versus LOF tolerance. (biomedcentral.com)
Eleven potentially regulatory variants and two missense mutations were identified. (fiocruz.br)
Genetically speaking, one point mutation changes the transcription factor so that the phenotype of our gene regulatory system changes by X, and the other point mutation changes the binding site so that the phenotype changes by Y. Now, when both mutations occur together, the phenotype is not simply X+Y, it is different. (ist.ac.at)
In this study, the researchers give a mechanistic understanding of how the mutations in two different molecules interact, explains Mato Lagator: "Most excitingly, we show that - in this gene regulatory system - most of the epistasis arises from the genetic structure of the system. (ist.ac.at)
We are investigating the impact of specific classes of gene mutations, such as ATM, BRCA1, and MYBL2 on genome integrity. (birmingham.ac.uk)
Somatic mutations were identified in NXK2-5 and its molecular partners, TBX5 and GATA4 , as well as the transcription factor HEY2 in formalin fixed tissue taken from a collection of hearts with atrial septal defects (ASD), 8 ventricular septal defects (VSD), and atrioventricular canal defects (AVCD). (cdc.gov)
and (3) Rapp-Hodgkin syndrome, all of which are caused by mutations in the TP63 gene. (medscape.com)
Better understanding of new mutations and the wide range of possible phenotypes led to the development of a new nomenclature proposal, based on the gene and inheritance pattern. (medscape.com)
[ 6 ] However, the gene mutations responsible for the different forms of CMT1 are clearly myelin genes. (medscape.com)
Denys-Drash syndrome (DDS) is a rare disorder consisting of the triad of congenital nephropathy, Wilms tumor , and intersex disorders resulting from mutations in the Wilms tumor suppressor ( WT1 ) gene. (medscape.com)
Denys-Drash syndrome is the result of mutations in the WT1 gene on chromosome band 11p13. (medscape.com)
Point mutations in the WT1 gene result in loss of its regulatory function, with the consequent abnormalities in glomerular formation and gonadal differentiation seen in Denys-Drash syndrome. (medscape.com)
Mutations that disrupt the second alternative splicing site of the WT1 gene alter the normal ratio of KTS-positive/negative isoforms from 2:1 to 1:2 and result in abnormalities in glomerular formation and gonadal differentiation seen in Frasier syndrome. (medscape.com)

Pharmacogenetic studies have been also performed in order to evaluate the role of host genetic variants in the prediction of recurrence risk and response to adjuvant treatment with FLs and OXA. (frontiersin.org)
Specifically, a long gene typically has a large expected number of LOF variants under a neutral mutation model. (biomedcentral.com)
This mouse population segregates millions of variants from eight inbred founders, enabling precision genetic mapping with extensive genotypic and phenotypic diversity. (elifesciences.org)
Our results demonstrate that statistical interactions between genetic variants and chromatin accessibility are common throughout the genome. (elifesciences.org)
Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr. (fiocruz.br)
Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. (fiocruz.br)
Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes. (fiocruz.br)
Genetic variants with gene regulatory effects are associated with diisocyanate -induced asthma. (cdc.gov)
Objective: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. (cdc.gov)
Four variants exhibited effects on gene regulation (ATF rs11571537, CDH17 rs2446824 and rs2513789, and TACR1 rs2287231). (cdc.gov)
These results demonstrate that many DA-associated genetic variants likely act by modulating gene regulation. (cdc.gov)
Approximately 70% of the genetic risk associated with breast cancer is still unaccounted for and it is predicted that the remainder of susceptibility loci will include common, low-effect variants that most likely have regulatory effects. (springer.com)
Polymorphic variants at regulatory elements can cause differential allelic expression (DAE), thus using DAE as a quantitative trait could help identify such variation. (springer.com)
In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. (escholarship.org)
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. (kb.se)
In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. (lu.se)
Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. (lu.se)
We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. (lu.se)

DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. (lu.se)
Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. (nature.com)
For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs), and 62,305 trans-eQTL, with the majority showing cell type specific effects on gene expression. (iscb.org)
This advantage enables more efficient gene modulation and labeling of chromosomal loci in live cells. (jax.org)
Differential allelic expression (DAE) in heterozygote individuals could be used to develop a new approach to discover regulatory breast cancer susceptibility loci. (springer.com)
These loci are enriched in regions of open chromatin, histone modifications, and transcription factor binding, suggesting that they represent regions of the genome that are actively transcribed in the human heart. (uni-muenchen.de)
We further highlighted 67 candidate genes at the identified loci that are preferentially expressed in cardiac tissue and associated with cardiac abnormalities in Drosophila melanogaster and Mus musculus. (uni-muenchen.de)
The immune system consists of a large number of molecules and processes, and immunodeficiencies can therefore be caused by genetic alterations at many loci. (lu.se)

Gene-Expression Analysis of Cell-Cycle Regulation Genes in Virus-Infected Rice Leaves. (routledge.com)
Genetic regulatory circuits are analogous in many ways to electronic circuits in how they use signal inputs and outputs to determine gene regulation. (wikipedia.org)
Like electronic circuits, their organization determines their efficiency, and this has been demonstrated in circuits working in series to have a greater sensitivity of gene regulation. (wikipedia.org)
We also found an unexpectedly dynamic pattern of transcript isoform regulation, suggesting a critical regulatory role during HSC differentiation, and a cell cycle/DNA repair signature associated with multipotency in MPP2 cells. (lu.se)
The process of turning genes on and off is known as gene regulation. (medlineplus.gov)
Gene regulation is an important part of normal development. (medlineplus.gov)
Gene regulation also allows cells to react quickly to changes in their environments. (medlineplus.gov)
Although we know that the regulation of genes is critical for life, this complex process is not yet fully understood. (medlineplus.gov)
Gene regulation can occur at any point during gene expression, but most commonly occurs at the level of transcription (when the information in a gene's DNA is passed to mRNA). (medlineplus.gov)
The National Human Genome Research Institute provides a definition of gene regulation in their Talking Glossary of Genetic Terms. (medlineplus.gov)
The Khan Academy has an educational unit on gene regulation , including videos about gene regulation in bacteria and eukaryotes. (medlineplus.gov)
Understanding the scope and landscape of these interactions on a genome-wide scale is a vital step towards deciphering the genetic regulation of gene expression and, in turn, the mechanisms of non-coding variation on phenotypic outcomes. (elifesciences.org)
Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. (upm.es)
People and mice share the same keratin genes, and what makes us different is how they are switched on, with variations in regulation that produce furry mice and mostly hairless people. (freethoughtblogs.com)
A new gene regulation and labeling platform dubbed "Casilio" can simultaneously execute distinct functions at multiple areas of the genome at the same time, expanding researchers' ability to study gene function and chromosome structure, Jackson Laboratory (JAX) researchers report. (jax.org)
They examined tissue taken from the gills - an important osmoregulatory organ in fish - and generated DNA and RNA sequence data to study the activity, regulation, and function of different genes. (thefishsite.com)
At least 60 genes have been described as participants in flowering regulation [ 9 ]. (biomedcentral.com)
[ 8 ] Other classification systems categorize the ectodermal dysplasias based on defects in cell-cell communication and signaling, adhesion, transcription regulation, or development. (medscape.com)

The whole mitogenome of O. conispadiceus is 16,027 basepairs (bp) in length with a base composition of 41.4% A, 34.8% T, 16.1% C, 7.7% G and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a major non-coding region (MNR). (tonmo.com)

Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)
The fully sequenced genome, since compact and unduplicated, gives acces to regulatory DNA segments, isolated for reporter gene essays in vivo . (uibk.ac.at)
Remarkable progress in science and technology has led to the development of powerful tools for genome sequencing and editing increasing ability to study gene expression and function at multiple levels from cells to populations. (cdc.gov)
Sub-objective 4.1: Analysis of ExPEC isolated from chickens and humans: biofilm assays, virulence gene profiles, antimicrobial resistance profiles, whole genome comparison of ExPEC strains isolated from chicken and human infections. (usda.gov)
While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome. (biomedcentral.com)
Analyses of these interactions has previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. (elifesciences.org)
Here we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. (elifesciences.org)
With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. (elifesciences.org)
We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. (elifesciences.org)
Local regulatory mechanisms within the genome and their interaction with chromatin structure give rise to subtle variations in gene expression. (elifesciences.org)
Yet the interacting effects that genetic and epigenetic factors produce on gene transcription are rarely studied at a genome-wide scale, leaving us without global information on a key step between the genetic code and the phenotype. (elifesciences.org)
Physical distance along a linear genome is a common metric for determining whether a putative regulatory element will affect a given gene's transcription. (elifesciences.org)
In this work, we analyzed the protein composition of four strains (wild type, FnrP-, NNR- and NarR-mutant strains) grown aerobically, semiaerobically and semiaerobically in the presence of nitrate to discover the global role of FNR-family transcription regulators using proteomics, with data validation at the transcript and genome levels. (nih.gov)
Evo-devo proponents have been arguing that the most important changes in evolution have been in the regulatory elements of the genome, in particular the stretches of DNA called cis-regulatory elements (CREs) that flank the coding regions. (freethoughtblogs.com)
The widely used CRISPR-Cas9 gene-editing technology has enabled researchers to alter genome sequence or gene expression with great precision, says JAX Assistant Professor Albert Cheng, Ph.D., first and co-corresponding author of a paper published in Cell Research . (jax.org)
The team optimised a genome sequencing approach that reveals the activity of potential transcription factor binding sites and genetic switches for turning expression on and off. (thefishsite.com)
Their approach identified regions of the genome they believe are responsible for controlling the activity of certain osmoregulatory genes, which in turn influence the function of the gills and how the fish responds to changing water conditions. (thefishsite.com)
Since the antibody also included a staining molecule, they could home in on potential TRF1-targeted genes by scanning the fly genome for regions that were preferentially stained. (sciencedaily.com)
However, if you look at the genome of the fly, it's about 12,000 genes. (sciencedaily.com)
We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. (kb.se)
While each DNA blueprint, or gene, encodes for a different machine or structure, the genome, the collection of DNA wrapped up inside the nucleus, is much more active than a quiet library of neatly stacked blue-prints. (birmingham.ac.uk)
We examine the impact that processes such as transcription and replication have on genome stability. (birmingham.ac.uk)

Pooled CRISPR screen is a promising tool in drug targets or essential genes identification combined with different phenotype readouts. (hep.com.cn)

These circuits can be modelled in silico to predict the dynamics of a genetic system. (wikipedia.org)

This told us that our hypothesis that TRF1 was specialized for certain genes was on the right track. (sciencedaily.com)
Lu's lab now hopes to use this approach to study cellular processes that are controlled by a series of events, such as the appearance of cytokines or other signaling molecules, or the activation of certain genes. (sciencedaily.com)
Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)

B) Histone marking on the regulatory region of EC master transcription factors was switched following the order, (1) release the brake mark and then (2) enter the acceleration mark. (medicalxpress.com)
They found that the histone code, which alters the transcriptional state of the gene, changes over time as stem cells differentiate into blood vessels in response to a stimulus. (medicalxpress.com)
Furthermore, an examination of the histone code revealed that the regulatory genomic region of the transcription factors (ETS/GATA/SOX) was found to have gradually switched from a "brake histone mark," which suppresses transcription, to an "accelerator histone mark," which activates transcription, while in the process of differentiating into the vascular endothelium. (medicalxpress.com)
Previously, in the region that controls the function of the transcription factor that promotes differentiation from ES cells to a specific cell type, bivalent modifications of histones such as the accelerator and brake histone marks for transcription were thought to have coexisted. (medicalxpress.com)
Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. (bvsalud.org)

They are functional clusters of genes that impact each other's expression through inducible transcription factors and cis-regulatory elements. (wikipedia.org)
Efficient functional readout, notably at DNA level in vivo is often complicated by the complexity of regulatory interactions and the complexity of genomes, particularly in vertebrates. (uibk.ac.at)
Such DNA constructs, when electroporated in fertilised eggs, produce transiently transgenic embryos and allow rapid gene functional and gene regulatory analyses , in precisely identifyable tissue precursors, from earliest embryonic stages in vivo . (uibk.ac.at)
The project aims to identify genes that are required for a functional AZ, and to understand how modification of these genes causes morphological differences in the AZ in different species. (usda.gov)
Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. (biomedcentral.com)
Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. (biomedcentral.com)
Our method integrates a population genomics-based approach with a functional genomics approach, providing unparalleled ability to predict LOF intolerance, particularly in short genes. (biomedcentral.com)
The role of these candidates is tested using gene knock-out plants and functional characterization of confirmed candidates is performed using a combination of physiological, biochemical and genetic approaches. (mpg.de)
These findings suggest a functional role of AP-2 transcription factors in preventing lactogenesis. (biomedcentral.com)

Analysis of gene activity in these microstructures enabled the researchers to conclude that Ap4 acts on two crucial signaling pathways that regulate the balance between stem cell maintenance and differentiation, and tips the scales toward stem cells. (medicalxpress.com)
Introduction regulate choices of expressed genes as part of the macrophage/ neutrophil lineage. (lu.se)
Working with JAX Distinguished Visiting Professor Haoyi Wang, Ph.D., and other colleagues, Cheng was looking for a way to regulate multiple genes in the mouse and other cell and animal models. (jax.org)
Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been reported. (biomedcentral.com)

In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. (elifesciences.org)
We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in developmental timing. (bvsalud.org)
This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. (biomedcentral.com)

To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1) was used. (upm.es)
As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element) that is sufficient to drive strong expression of a reporter gene in planta. (upm.es)
In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis- and trans-regulatory codes. (upm.es)
According to Tjian, the discovery of tandem promoters represents the opening of a new terrain for the exploration of transcription control. (sciencedaily.com)
They share a conserved structure and control gene expression by binding to the respective promoters as homo- or heterodimers. (biomedcentral.com)

Secretory epithelial cells display lactogenic differentiation which is characterized by the expression of milk protein genes, such as beta-casein or whey acidic protein (WAP). (biomedcentral.com)
Differentiating HC11 cells displayed lower expression levels of milk protein genes than mammary glands of mid-pregnant or lactating mice. (biomedcentral.com)
The lactogenic differentiation of the secretory epithelial cells is characterized by the synthesis of lactose and milk fat and by the expression of milk protein genes, such as beta-casein or whey acidic protein (WAP). (biomedcentral.com)

Gene Ontology (GO) enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle. (biomedcentral.com)

They also use inputs such as trans and cis sequence regulators of genes, and outputs such as gene expression level. (wikipedia.org)
To determine whether the extensive rewiring comes from changes in cis-regulatory modules, the upstream and downstream regulators of two conserved transcription factors, YAB2/SH1 and MYB26, will be characterized in the genetically tractable species Setaria and Brachypodium, with a combination of mutant analysis, RNA-seq, DAP-seq and bioinformatics. (usda.gov)
Unlike sequence-specific transcription factors, epigenetic regulators do not necessarily bind DNA at consensus sequences, but still achieve reproducible target binding in a manner that is cell and maturation-type specific. (frontiersin.org)
A growing body of evidence indicates that epigenetic regulators rely, amongst other factors, on their interaction with untranslated RNA molecules for guidance to particular targets on DNA. (frontiersin.org)
The switch from aerobic to anaerobic respiration in the bacterium Paracoccus denitrificans is orchestrated by the action of three FNR-type transcription regulators FnrP, NNR and NarR, which are sensors for oxygen, nitric oxide and nitrite, respectively. (nih.gov)
The next steps are to use similar genomic approaches to find genes and their regulators associated with other traits of interest for aquaculture, like growth and disease resistance. (thefishsite.com)

We focus on novel combinatorial codes for transcription factors as nuclear effectors of major signaling pathways, including Wnt and FGF/MEK signaling. (uibk.ac.at)
Finally, these pathways have been associated with external exposure factors such as exposure to chemicals and air pollution, the role of diet and the presence of beneficial nutrients, as well as the overall health status. (aiche.org)
CONCLUSIONS Taken together, our findings provide new insights into genes and biological pathways controlling myocardial mass and may help identify novel therapeutic targets. (uni-muenchen.de)
It has been reported that various hosts recognize lipopolysaccharides in the cell membrane structure through TLR9 and activate downstream mitogen-activated protein kinase (MAPK) and nuclear transcription factor- κ B (NF- κ B) pathways mediated by MyD88 to promote the MAPK protein phosphorylation, and NF- κ B enters the nucleus, further releasing cellular inflammatory factors [ 12 ]. (hindawi.com)
Consequently, the transition to flowering is under strict genetic and environmental control [ 1 ], with floral initiation being induced by both external (photoperiod- and vernalization-dependent) and internal pathways (autonomous, age- and gibberellin-dependent) [ 2 - 4 ]. (biomedcentral.com)

2) the genetic and molecular basis for ascidian bioadhesion motivated by the search for novel biomimetic reagents. (uibk.ac.at)
The omic data will also reveal genetic markers for identification, molecular typing, and detection of these pathogens. (usda.gov)
We are investigating the molecular consequences of HNT and the basis of the varying tolerance using a wide range of physiological approaches in addition to metabolite, enzyme activity and gene expression profiling. (mpg.de)
These results provide unique insight into the GRAS family of TFs and novel regulatory targets for further molecular characterization. (usda.gov)
Like discovering a car that has more than one engine under the hood, cell biologists are learning to their surprise that alternate molecular machines can drive the basic process of transcription that orchestrates the expression of genes. (sciencedaily.com)

To determine if the disparate early regulatory networks converge on a conserved late stage set of genetic interactions, transcriptomic, enzymatic, and cell wall changes will be evaluated right before and after abscission. (usda.gov)
Exposome research tries to reverse the paradigm of â nature versus nurtureâ and adopt one defined by complex and dynamic interactions between DNA sequence, epigenetic DNA modifications, gene expression and environmental factors that all combine to influence disease phenotypes. (aiche.org)
Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. (elifesciences.org)
We found that these interactions occur within the local area of the affected gene, and that this locality corresponds to topologically associated domains (TADs). (elifesciences.org)
Genetic analyses are a powerful approach that allow the study of these interactions. (elifesciences.org)
This has led to the concept of a "local area" in which most regulatory interactions take place. (elifesciences.org)
The number, position and interactions between cis-elements and transcription factors (TFs) determine the expression pattern of a gene. (upm.es)
Dynamical models based upon known interactions between these master genes, such as mutual antagonism and autoregulation, fail to make the system bistable, a desired feature for robust lineage determination. (lu.se)

The AZ of three distantly related grass species (weedy rice, Brachypodium, and Setaria) is controlled by distinct sets of genes, suggesting rewiring of the underlying genetic network. (usda.gov)
But hang on, the non-evo-devo people rightly cry, while mice and humans might have very similar sets of genes, the coding regions of those genes are not identical, and it is premature to claim that those differences are relatively insignificant … and we also know of variations in coding sequences that make big differences in fitness. (freethoughtblogs.com)

In addition to environmental factors, phenotypes can also respond to genetic perturbations in a plastic or homeostatic manner, which characterizes the potential of an organism to express phenotypes when genes mutate. (nature.com)
These genes were selected based on their role in asthmatic inflammatory processes and History previously reported associations with asthma phenotypes. (cdc.gov)
Of these mediators, cytokines play a single nucleotide polymorphisms (SNP) in pro-inflammatory cytokine genes and asthma phenotypes (Che et al. (cdc.gov)

Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. (nature.com)
Change in genetic variation across environments is one of the many forms of genotype by environment interaction (G×E). G×E can be interpreted equivalently either as variable genetic architecture across environments or as variable environmental plasticity across genotypes, depending on what factor is chosen as the context. (nature.com)

The dynamics of genetic variation (variance across different genotypes) and environmental variation (variance across different environments) may be controlled by different mechanisms. (nature.com)
To unravel fundamental genetic mechanisms that control cell fate choice in vivo , we study embryonic development in a simple marine invertebrate, the ascidian Ciona intestinalis , belonging to the vertebrate sister group, the tunicates. (uibk.ac.at)
1) the mechanisms and dynamics for gene regulatory switches affecting the pluripotent ectoderm in vivo . (uibk.ac.at)
Building on our previous research, we will investigate strain diversity and mechanisms of tolerance to stresses, including acid and exposure to antimicrobial compounds, as well as investigate factors affecting attachment and biofilm formation of Campylobacter. (usda.gov)
Thus, understanding the interplay among environmental and genetic factors, in relation to the respective involved mechanisms, is the cornerstone of targeted interventions, both at individual and community level. (aiche.org)
The work will be of broad interest to geneticists and those working to understand the basic mechanisms of gene expression. (elifesciences.org)
Ranking of DA-associated SNPs based on their likelihood to affect gene regulatory mechanisms in the lung yielded 21 prioritized SNPs. (cdc.gov)

The rationale behind these prediction methods is that essential genes, with minimal inter-individual variation, are subject to purifying selection in order to maintain their sequence in the population, as alterations would lead to reduced fitness. (biomedcentral.com)
For example, it can be fused to domains that activate or repress gene expression, allowing researchers to increase or decrease gene expression at will without changing the actual sequence. (jax.org)
Many diseases involve variations in gene expression rather than genetic sequence. (jax.org)
Today we use epigenetics to mean changes to gene expression that are not caused by changes in the actual DNA sequence. (lu.se)
Gene expression is the process of several steps through which the information in a gene's DNA sequence is transferred to the structures and functions of a cell. (lu.se)
In front of every gene is a DNA sequence called a promoter. (lu.se)

We therefore suggest a new mechanism involving a cofactor that is regulated as well as recruited by one of the master genes to bind to the antagonistic partner that is necessary for bistability and hence switch-like behavior. (lu.se)
Transcription factors bind alongside the promoter and set off the gene expression. (lu.se)
Certain transcription factors do not bind when the DNA is methylated while others only bind when the DNA is methylated. (lu.se)

We recently discovered new ways the BRCA1 gene functions which could help expand our understanding of the development of ovarian and breast cancers. (birmingham.ac.uk)

Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. (biomedcentral.com)
Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. (biomedcentral.com)
Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods. (biomedcentral.com)
The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes. (biomedcentral.com)

This important work substantially advances our understanding of the interplay between genetic variation, chromatin, and genes within topologically associated domains and how this interplay regulates gene expression. (elifesciences.org)
But when we take a system composed of several components, such as a system that regulates gene expression, what happens when not only a single component is mutated, but several? (ist.ac.at)

Clinical and genetic analyses of a Swedish patient series diagnosed with ataxia. (lu.se)

We analyzed gene expression during Arabidopsis thaliana meristem development under long day conditions from day 7 to 16 after germination in one-day increments. (biomedcentral.com)

Researchers at the Institute of Science and Technology Austria (IST Austria) found that in a gene regulatory system in the bacterium Escherichia coli, the more components that are mutated, the more freely the system can evolve. (ist.ac.at)
The researchers then identified genetic differences at gene regulatory regions in the Nile tilapia and 27 other tilapia species. (thefishsite.com)
The researchers identified several genes relevant to traits that help tilapia to tolerate saltier water and acclimatise to freshwater. (thefishsite.com)
Although the reason for multiple transcriptional controls remains mysterious, researchers speculate that the mechanism might allow the same gene to be used for different purposes in different cells. (sciencedaily.com)
Now, Howard Hughes Medical Institute (HHMI) researchers have taken an important step in understanding this phenomenon by pinpointing the first gene in the fruit fly Drosophil melanogaster that is a target of an alternate control molecule, called TRF1. (sciencedaily.com)
To attempt to pinpoint a particular TRF1-responsive gene from among the 12,000 known Drosophila genes, the researchers first launched an "aerial reconnaissance" of Drosophila chromosomes. (sciencedaily.com)
After creating circuits that could record events, the researchers then incorporated genes into the array of recombinase binding sites, along with genetic regulatory elements. (sciencedaily.com)

In an article in the May 5, 2000, issue of the journal Science, HHMI investigator Robert Tjian and graduate student Michael C. Holmes report that the Drosophila gene tudor contains tandem promoter segments, one of which responds to TRF1. (sciencedaily.com)
Screening those genes revealed that the Drosophila gene tudor is a potential target gene that can be activated by TRF1. (sciencedaily.com)

Genetic regulatory circuits (also referred to as transcriptional regulatory circuits) is a concept that evolved from the Operon Model discovered by François Jacob and Jacques Monod. (wikipedia.org)
Genetic regulatory circuits also have an ability to be evolutionarily rewired without the loss of the original transcriptional output level. (wikipedia.org)
The scientists had found evidence that TRF1 is apparently one of several alternate transcriptional control molecules-called recognition factors-that can replace the most prevalent control element, called TATA-binding protein, or TBP. (sciencedaily.com)

The genetic regulatory network consisting of the Oct4, Nanog, and TET transcription factors (TF's) is understood to control cell fate, specifically the transitions between somatic and pluripotent states. (aps.org)

Dynamically and epigenetically coordinated gata/ets/sox transcription factor expression is indispensable for endothelial cell differentiation. (medicalxpress.com)
Furthermore, they found that a transcription factor group essential for blood vessel differentiation (ETS/GATA/SOX) has a previously unknown role. (medicalxpress.com)
Schematic representation of the genetic regulatory network linking four transcription factors and EC differentiation. (medicalxpress.com)
Transcription factors SOX and FLI1, both important for endothelial differentiation, were induced between 12 and 24 hours. (medicalxpress.com)
At 48 hours, after differentiation into vascular endothelium was determined, a system of transcription was established in which genes unique to vascular endothelial differentiation were induced. (medicalxpress.com)
The overall methodology is being verified in a series of population studies across Europe, tackling various levels of environmental exposure, age windows and gender differentiation of exposure, and socio-economic and genetic variability. (aiche.org)
Transcription factors AP-2alpha and AP-2gamma are downregulated during lactation, and their overexpression in transgenic mice impaired the secretory differentiation of the mammary epithelium, resulting in lactation failure. (biomedcentral.com)
Using RT-PCR we could not detect a downregulation of any of these genes during the lactogenic differentiation of HC11 cells in vitro. (biomedcentral.com)
Downregulation of AP-2 transcription factor genes is not required for lactogenic differentiation of HC11 cells but may functionally be involved in aspects of lactogenic differentiation in vivo that are not reflected by the HC11 system. (biomedcentral.com)
In this report we analyzed AP-2 transcription factor expression in HC11 cells subjected to lactogenic differentiation conditions. (biomedcentral.com)
The WT1 protein mediates the mesenchymal-epithelial transition and differentiation during morphogenesis of the kidney and gonad by repressing genes that encode cell proliferation factors and by activating genes that encode markers of epithelial cell differentiation. (medscape.com)

Our starting point is a mechanistic model formulated in the language of chemical reaction networks that describe promoter binding together with transcription/translation. (aps.org)
While a full complement of open chromatin, epigenetic, and TF-binding experiments provide information for likely candidate regulatory regions, using TF-binding approaches such as ChIP-seq or DAP-seq can provide additional valuable insight and targets for reverse genetic approaches such as EMS-induced or natural SNP variant screens or CRISPR editing techniques (e.g. promoter bashing). (usda.gov)
DNA constructs were cloned into a pGL3 promoter vector for luciferase gene reporter assays. (cdc.gov)
We thought that these genes would either have a TBP-responding promoter or a TRF-responding promoter. (sciencedaily.com)

Studies are generally limited to examination of individual regions or overlapping single-nucleotide polymorphisms (SNPs) and open chromatin peaks with limited investigation into how these regulatory elements combine to affect gene transcription 1 , 2 . (elifesciences.org)

Analysis of mutants with abnormal flowering time has allowed the identification of genes controlling floral transition [ 8 ]. (biomedcentral.com)
With the recent identification of the causative genetic defect for a number of the ectodermal dysplasias, newer classification systems have been devised. (medscape.com)

Patients were genotyped for a panel of 192 tagging polymorphisms in 34 immune-related genes. (frontiersin.org)
Regulatory polymorphisms in cis-acting elements result in the unequal expression of alleles. (springer.com)
We aimed to perform a more extensive evaluation of differential allelic expression between blood and breast in order to assess the potential usefulness of LCL and fresh blood in association studies, to identify regulatory polymorphisms related to susceptibility to breast cancer. (springer.com)

High-Throughput Approaches for Characterization and Efficient Use of Plant Genetic Resources. (routledge.com)
Objective 4: Phenotypic and genetic characterization of extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from poultry and produce. (usda.gov)

Identifying non-coding regions that control gene expression has become an essential aspect of understanding gene regulatory networks that can play a role in crop improvements such as crop manipulation, stress response, and plant evolution. (usda.gov)

We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. (springer.com)
Candidate genes that could help fish to tolerate warmer and saltier water have been identified in new research from the Earlham Institute, potentially providing a vital resource to guide breeding programmes in freshwater aquaculture. (thefishsite.com)
2 - 4 Because of its critical role in cardiogenesis, NKX2-5 has been a prime candidate in studies to identify the genetic basis of structural congenital heart defects. (cdc.gov)

Importantly, the state of plasticity or homeostasis, with respect to either genetic or environmental variation, is not necessarily static and can be modified by both genetic and environmental factors. (nature.com)
This work brings together genetic epidemiology with scRNA-seq to uncover drivers of inter-individual variation in the immune system. (iscb.org)
Greater availability of African genomes will improve our understanding of the role of genomic variation in genetic diseases and common complex diseases in all populations. (cdc.gov)
Conversely, phenotypic variation in genetically diverse populations is a result of both genetic and epigenetic factors operating in tandem. (elifesciences.org)
Normal gene expression variation is thought to play a central role in inter-individual variation and susceptibility to disease. (springer.com)

Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. (lu.se)
Differential gene expression analysis identified a number of root-specific CYP genes. (techscience.com)
We discovered an unprecedented burst of differential expression of cell cycle related genes at one particular point during transition to flowering. (biomedcentral.com)

These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention. (kb.se)
These results suggest that genetic variations in TNF, TGFB1, PTGS1 and PTGS2 genes contribute to DA susceptibility. (cdc.gov)

Transcription Factors, Gene Regulatory Networks, and Agronomic Traits. (routledge.com)
In plant synthetic biology, genetic regulatory circuits can be used to program traits to increase crop plant efficiency by increasing their robustness to environmental stressors. (wikipedia.org)
By characterising the genes responsible for these desirable traits, we can now share these new resources with freshwater fish farms to help guide selective breeding programmes. (thefishsite.com)

However, a growing body of evidence suggests that recruitment, stability, and function of epigenetic factors can be mediated by non-protein-coding RNAs. (frontiersin.org)
These findings provide evidence that genetic and epigenetic factors operate within the context of three-dimensional chromatin structure. (elifesciences.org)

Recently, the expansion of high-quality reference genomes and chromatin profiling techniques have opened up direct and comparative accounting of transcription factor (TF) binding locations that could modulate proximal or distal gene expression. (usda.gov)

The WT1 protein is a transcription factor predominantly expressed in the embryonic kidneys and gonads. (medscape.com)

The lactose utilization (lac) operon of Escherichia coli was shown to specify three enzymes and a regulatory locus, initially posited to express an RNA, but subsequently found to encode a DNA-binding repressor protein that is displaced upon lactose binding. (taylorfrancis.com)
The key integrator of the vernalization pathway is a MADS-box transcription factor, FLOWERING LOCUS C ( FLC ), which functions as a repressor of flowering and whose expression decreases during vernalization [ 24 ]. (biomedcentral.com)

Among the targets of c-MYC is the gene AP4, which codes for the transcription factor of the same name (AP4). (medicalxpress.com)

The NKX2-5 gene on chromosome 5q34 consists of two exons which encode a 324 amino acid protein. (cdc.gov)

Emergence of human G2P[4] rotaviruses containing animal derived gene segments in the post-vaccine era. (cdc.gov)

Because epigenetic changes are essentially reversible - unlike genetic changes - the starting point for the search for drugs is that epigenetically inactivated genes can be reactivated (and vice versa) if only the right molecule is added. (lu.se)

By modeling these associations between mutational signature and gene expression, mutational signatures can be potentially inferred in future RNA-seq studies. (hep.com.cn)

Biochemical studies suggest that in one case this transcription factors to implement particular genetic programs. (lu.se)

Shimeld, S.M. (2022): Hmx gene conservation identifies the origin of vertebrate cranial ganglia. (uibk.ac.at)
Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi. (cdc.gov)

The latter pair inherits the state of its upstream master genes and further reinforces the decision due to several feedback loops, thereby leading to irreversible commitment. (lu.se)

Stem cell treatments, such as those affecting the states of the network of pluripotency genes, are expected to play a central role in future personalized medicine. (aps.org)
The c-MYC transcription factor controls the activity of a large number of genes involved in cell division, and its over-expression leads to excessive cell proliferation. (medicalxpress.com)
Each cell expresses, or turns on, only a fraction of its genes at any given time. (medlineplus.gov)
Genes are turned on and off in different patterns during development to make a brain cell look and act different from a liver cell or a muscle cell, for example. (medlineplus.gov)
Hematopoietic stem cell lineage choices are decided by genetic networks that are turned ON/OFF in a switch-like manner. (lu.se)
However, prior to commitment, it has been cells, it is evident that GATA-1 and PU.1 are able to specify observed that many genes are expressed at intermediate or basal erythroid and myeloid cell fates (see [16] and references therein). (lu.se)
But most cell functions are more complex than that-being regulated by multiple genes. (jax.org)
A Toll-like receptor (TLR) is a transmembrane protein encoded by the Toll gene, which is one of cell transmembrane receptors and pathogen pattern recognition receptors (PRRs) in the innate immune system [ 9 ]. (hindawi.com)
The gene expression varies between different types of cell and when these epigenetic changes are inherited by daughter cells through cell division in the womb, different tissues and organs are built. (lu.se)

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. (cdc.gov)

However, the structure of the circuits have shown to not be a reliable indicator of the function that the regulatory circuit provides for the larger cellular regulatory network. (wikipedia.org)
These biological gene circuits can be used synthetically to act as physical models for studying regulatory function. (wikipedia.org)
Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer. (escholarship.org)
DNA methylation is a chemical process that regulates the function of the genes. (lu.se)
The precise ratio of the KTS-positive/negative isoforms seems to be crucial for the normal function of the WT1 gene. (medscape.com)

Genes with higher network connectivity are under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness. (nature.com)
Implementing large scale studies across different populations could substantially enhance efforts to uncover the role of genetic factors in various diseases. (cdc.gov)
The regulatory protein c-MYC plays an important role in promoting the development of many types of tumors. (medicalxpress.com)
It is likely that many other factors play a role. (blogspot.com)
Genetic factors might play a substantial role in the incidence of YEL-AVD. (cdc.gov)

Anatomy16

Organisms8

Chemicals and Drugs127

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Phenomena and Processes82

Disciplines and Occupations1

Information Science4

Proteins23

Target genes6

Mutations21

Variants18

Loci8

Regulation18

Protein-codin1

Genome22

Phenotype1

Modelled in silico1

Certain genes3

Histone5

Functional9

Regulate4

Developmental3

Promoters5

Milk protein genes3

Enrichment1

Regulators6

Pathways5

Molecular5

Interactions8

Sets of genes2

Phenotypes3

Genotype2

Mechanisms7

Sequence6

Bind3

BRCA11

Essential genes4

Regulates gene expression2

Analyses1

Arabidopsis1

Researchers7

Drosophila2

Transcriptional3

Somatic1

Differentiation11

Promoter4

Affect gene1

Identification2

Polymorphisms3

Characterization2

Control gene expression1

Candidate3

Variation5

Differential3

Susceptibility2

Traits3

Epigenetic factors2

Proximal1

Embryonic1

Locus2

Targets1

Chromosome1

Segments1

Epigenetically1

Potentially1

Biochemical1

Conservation2

Upstream1

Cell9

RRNA1

Function5

Role5