Transcription factor binding and chromatin. Medical search. Frequent questions

Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. (cellsignal.com)
In addition, loss of protein binding during the chromatin digestion and immunoprecipitation steps may bias the data or impede proper analyses. (cellsignal.com)
Once the chromatin immunoprecipitation itself is complete, several downstream analyses can be conducted on the purified chromatin and the associated proteins, histones, transcription factors, and cofactors. (cellsignal.com)
The Imprint Ultra Chromatin IP Kit is Sigma′s second generation chromatin immunoprecipitation (ChIP) kit developed for maximum sensitivity and optimum next-generation sequencing results. (sigmaaldrich.com)
It provides a complete solution for Chromatin Immunoprecipitation, including columns and reagents for DNA purification. (sigmaaldrich.com)
Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. (spandidos-publications.com)
Chromatin immunoprecipitation assays identified SOX2-binding sites on COL1A1 and COL1A2, indicating SOX2 as a transcription factor in collagen synthesis. (cdc.gov)
Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
Here, we develop a high-throughput indexed Chromatin ImmunoPrecipitation (iChIP) method coupled to massively parallel sequencing to systematically map protein-DNA interactions. (nih.gov)

Epigenetic mechanisms and transcription factor networks essential for differentiation of cardiac myocytes have been uncovered. (nature.com)
Among the epigenetic entities, DNA methylation is the best characterized and contributes to the transmission of the long-lasting transcription memory through cell division and therefore the phenotype. (selectbiosciences.com)
The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. (rsc.org)
In particular, I am involved in the data analysis of next-generation Illumina sequencing datasets of genome-wide transcription factor binding, epigenetic modifications and chromatin accessibility. (helsinki.fi)
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)
The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
Pharmacological reversal of the effects on chromatin structure completely eliminates the effects of maternal care on glucocorticoid receptor expression and hypothalamic-pituitary-adrenal (HPA) responses to stress, thus suggesting a causal relation between the maternally induced, epigenetic modification of the glucocorticoid receptor gene and the effects on stress responses in the offspring. (deepdyve.com)
Activated transcription factors in conjunction with chromatin remodelers induce epigenetic changes that reprogram IFN responses. (lu.se)
These findings suggest that the ROS-generated epigenetic mark 8-oxoGua via its reader OGG1 serves as a homeostatic thresholding factor in IFN-λ expression. (lu.se)
Epigenetic changes also take place throughout our lives as a result of normal ageing, lifestyle and environmental factors. (lu.se)
e.g. inflammation, genotoxicity, and This chapter focuses on issues as- ellers, growth factors, growth factor epigenetic alterations) and can have sociated with the understanding and receptors, signal transducers, and both genetic and epigenetic origins. (who.int)

scNMT-seq uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing (an adapted form of NOME-seq ). (epigenie.com)

The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. (nih.gov)
We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. (nih.gov)
For example, ChIP can be used to compare the presence of certain proteins at various loci, map the various proteins across a genomic region of interest, or quantify protein binding to an inducible gene in response to a stimulus over time. (cellsignal.com)
The principle behind ChIP is relatively straightforward and relies on the use of an antibody to isolate, or precipitate, a certain protein, histone, transcription factor, or cofactor and its bound chromatin from a protein mixture that was extracted from cells or tissues. (cellsignal.com)
In X-ChIP, chemical fixatives such as formaldehyde are used to crosslink the protein of interest to the DNA and fragmentation of chromatin is achieved through sonication or nuclease digestion. (cellsignal.com)
X-ChIP also minimizes the chances of chromatin protein loss during extraction, allowing for the detection of transient protein interactions. (cellsignal.com)
ChIP-PCR is performed to analyze histone modifications and/or protein binding to a known subset of target loci in the genome. (cellsignal.com)
NEW YORK (GenomeWeb) - A new microfluidics-driven DNA-protein binding assay has its creators dreaming of launching a startup to cash in on several potential applications. (genomeweb.com)
Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
GATA binding protein 3 (GATA3) is a zinc-finger pioneer transcription factor involved in diverse processes. (bmj.com)
The locus of Rubinstein-Taybi syndrome is located on band 16p13.3, which includes a gene encoding a binding protein for cyclic adenosine monophosphate-response element binding protein (CBP) ( CREBBP or CBP gene) that is responsible for the phenotype of Rubinstein-Taybi syndrome. (medscape.com)
BRDs can act as scaffolds that enable the recruitment of large protein complexes or they can act as transcription factors themselves. (frontiersin.org)
A family of histone acetyltransferases that is structurally-related to CREB-BINDING PROTEIN and to E1A-ASSOCIATED P300 PROTEIN. (bvsalud.org)
The gene that encodes the CREB binding protein, or CBP (also called CREBBP ), was cloned in 1995, and mutations in this gene have been found in some patients with Rubinstein-Taybi syndrome. (medscape.com)
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)
Lead also binds to metallothionein, a sulfhydryl-rich protein, but does not appear to displace cadmium or zinc. (cdc.gov)
They bind to structural components (emerin, nesprin), chromatin components (histone), signal transduction molecules (protein kinase C), and several gene regulatory molecules. (medscape.com)
Lastly, mutations in the transmembrane protein 43 (TMEM43), also termed LUMA, which binds to emerin and SUN2, has also been reported to cause an EDMD phenotype in a few families. (medscape.com)
Cas9 nuclease can be converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains 12 , 13 and then fused to transcription activation domains. (cdc.gov)

In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
That turned out to be really useful in order to express transcription factors that other assays have trouble working with. (genomeweb.com)
My area of expertise is in transcription factor biology using several genome-wide functional genomics methods (ChIP-seq/nexus, bulk/single-cell RNA-seq), chromatin conformation (ATAC-seq, DHS-seq), chromatin architecture methods (in situ HiC, ChIA-PET), cell fate conversion using transcription factors (transdifferention) and high-throughput enhancer assays (MPRAs such as STARR-seq). (helsinki.fi)
Who doesn't leave peanut butter and jam, chips and dip, and DNA methylation and chromatin assays? (epigenie.com)

NLRP7 thus appears to function in chromatin reprogramming and DNA methylation in the germline or early embryonic development, functions not previously associated with members of the NLRP family. (nih.gov)
In contrast, pathological gene expression in terminal heart failure is accompanied by changes in active histone marks without major alterations in CpG methylation and repressive chromatin marks. (nature.com)
Aberrant DNA methylation changes the genomic transcription, representing promising molecular targets for better cancer diagnostics and therapeutics. (selectbiosciences.com)
In this special feature, we highlight four new and exciting combinatorial DNA methylation/chromatin methods. (epigenie.com)
These talented teams wanted to avoid the need to infer where hits overlap when comparing DNA methylation and chromatin accessibility (ATAC-seq) data from two separate sets of cells. (epigenie.com)
The methods are particularly useful for identifying narrow windows where DNA methylation, chromatin state, and expression are not as tightly linked as ones thought. (epigenie.com)
The ATAC-Me paper shows that DNA methylation, chromatin accessibility, and DNA methylation can be uncoupled, where they change independently of one another during early development, with gene expression being linked to chromatin state and not DNA methylation. (epigenie.com)
EpiMethylTag was developed by the lab of Jane Skok at New York University to address the challenges associated with characterizing DNA methylation at transcription factor (TF) binding sites. (epigenie.com)
It is ideal for determining the DNA methylation status of transcription factor binding sites. (epigenie.com)
scNMT-seq (single-cell nucleosome, methylation, and transcription sequencing) is a triple threat developed by the labs of Wolf Reik (Babraham Institute, UK) and Oliver Stegle (EMBL-EBI, UK). (epigenie.com)
The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
DNA methylation alters glucocorticoid receptor expression through modifications of chromatin structure. (deepdyve.com)

The goal is to understand the role of these defined factors in modulating chromatin structure and gene expression during this dynamic process of transdifferentiation. (helsinki.fi)

ChIP utilizes antibodies that selectively recognize and bind proteins, including histones, histone modifications, transcription factors, and cofactors, to provide information about chromatin states and gene transcription. (cellsignal.com)
Histones play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. (fishersci.com)
Post translationally, histones are modified in a variety of ways to either directly change the chromatin structure or allow for the binding of specific transcription factors. (fishersci.com)
Bromodomains are proteins that contain modules of ~110 amino acids that recognize and bind acetylated lysine residues in histones and other proteins. (frontiersin.org)

We show that MORC proteins compact chromatin and reduce DNA accessibility to TFs, thereby repressing the transcription of stress-responsive genes. (biomedcentral.com)
In addition to mutations in TP53 and KRAS, we identify genetic alterations in chromatin remodelling genes, ARID1A and ARID1B, in histone methyltransferase MLL3, in histone deacetylase modifier SPOP and in chromatin assembly factor BAZ1A, in nearly two thirds of cases. (nih.gov)
In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and, consequently, expression of target genes. (biomedcentral.com)
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. (spandidos-publications.com)
Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1‑regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. (spandidos-publications.com)
In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. (spandidos-publications.com)
Transcriptional activity is regulated by DNA binding transcription factors, but these typically act in more than one cell lineage activating different subsets of target genes in each. (edu.au)
Both genes are highly conserved, and their proteins are thought to have 2 functions: (1) formation of a bridge or scaffold between the DNA-binding transcription factors and the RNA polymerase II complex and (2) serving as histone acetyltransferases that open the chromatin structure, a process essential for gene expression. (medscape.com)
These proteins are transcription factors, which means they attach (bind) to specific regions of DNA and help control the activity of particular genes. (medlineplus.gov)
Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. (nih.gov)
A second set of TFs bind already in the un-stimulated and preferentially target induced genes. (nih.gov)
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)
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)
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)

To elucidate the Nodal transcriptional network that governs endoderm formation, we used ChIP-seq to identify genomic targets for SMAD2/3, SMAD3, SMAD4, FOXH1 and the active and repressive chromatin marks, H3K4me3 and H3K27me3, in human embryonic stem cells (hESCs) and derived endoderm. (ca.gov)

In this talk, I will introduce Chromatin Interaction Analysis with Paired-End Tag sequencing (ChIA-PET), a next-generation sequencing-based method for identifying chromatin interactions between transcription factor binding sites on a genome-wide scale which was part of the ENCODE consortium. (selectbiosciences.com)
The kit allows researchers to explore the genome-wide binding sites of low abundance transcription factors (TFs), as well as novel histone modifications. (sigmaaldrich.com)
It is optimized for ChIP reactions with chromatin from 10 6 cells (up to ~50 μg DNA), and can also be scaled up (or several preparations pooled) to accommodate 10 8 cells for genome-wide binding studies in ChIP-chip and ChIP-Seq applications. (sigmaaldrich.com)
Also, experimental scientists interested in modern, cutting-edge functional genomics tools for epigenetics research in cancer, gene regulation by transcription factors in cancer, bioinformatics and computational analysis of genome-wide datasets are always encouraged to be in touch. (helsinki.fi)
Currently, my project focuses on understanding the epigenome repogramming during prostate cancer disease progression and role of lineage-specific transcription factors in modulating the 3D-genome architecture. (helsinki.fi)
We have also been successful in identifying regions of the genome bound by of histone modifications and transcription factors in hESCs and derived endoderm. (ca.gov)
While the role of Nodal is well defined within the context of endoderm commitment, mechanistically it is unknown how this signal is manifested at binding regions within the genome and how this signal interacts with chromatin state to trigger downstream responses. (ca.gov)
We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. (mendeley.com)
We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. (nih.gov)
Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)

Intensive study has demonstrated interactions with host-cell signal transduction and possibly eukaryotic transcription. (cdc.gov)

Our data demonstrates that transcription factors vary substantially in their binding dynamics, genomic localization, number of binding events, and degree of interaction with other factors. (nih.gov)

We find that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors, thereby repressing gene expression. (biomedcentral.com)
Chromatin accessibility measurements by ATAC-seq, together with transcription-factor DNA-binding preferences (motifs), can be used to broadly profile potential transcription factor binding events in relatively small populations of cells. (cincinnatichildrens.org)
I am involved in the computational analysis of RNA-seq data for gene expression, transcription factor binding, chromatin accessibility and functional enhnacer activity data. (helsinki.fi)
We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. (jci.org)

The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factors during erythroid differentiation. (rochester.edu)
Chromatin and Transcriptional Signatures for Nodal Signaling During Endoderm Formation in hESCs The first stages of embryonic differentiation are driven by signaling pathways hardwired to induce particular fates. (ca.gov)
We are currently pursuing studies of the dominant signaling and gene regulatory networks that control this process, including the Ras/MAPK cascade, which is required for stem cell-mediated self-renewal and the p53 transcription factor family member, p63, which is required for epidermal differentiation. (stanford.edu)

ChIP can be used to answer a multitude of scientific questions involving the interaction of proteins and chromatin. (cellsignal.com)
SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. (elifesciences.org)
In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)

Background: The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. (mendeley.com)
Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. (mendeley.com)
Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. (mendeley.com)
Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. (mendeley.com)
Conclusion: Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized. (mendeley.com)

The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
Here we present analysis of transcription factor binding motifs co-localized with non-coding variants. (biomedcentral.com)
Such stability of binding motifs is even more exhibited in DNase accessible regions. (biomedcentral.com)
Further analysis of transcription factors with conserved binding motifs can reveal cell regulatory pathways crucial for the survivability of various human cancers. (biomedcentral.com)
The binding location of the three GRAS TFs display unique and shared gene targets and categories of previously-characterized DNA-binding motifs as well as novel sequences that could potentially be GRAS family-specific recognition motifs and have been associated with gametogenesis, floral development, light signaling, hormone signaling, and root development. (usda.gov)

Our work uses functional genomics DNase-seq, ChIP-seq, RNA-seq, and chromatin state data to computationally identify combinations of transcription factor binding sites that operate to define the activity of cell-type specific enhancers. (hopkinsmedicine.org)

H3 along with four core histone proteins binds to DNA forming the structure of the nucleosome. (fishersci.com)

use chromatin modifications and transcription factors to predict transcription levels in Arabidopsis and rice. (plantae.org)

The first suggests that disruption of the inner nuclear membrane and the nuclear lamina causes disorganization of nuclear chromatin and gene expression, while the second proposes that the mechanical strength of the cell nucleus is disrupted when the nuclear lamina is weakened leading to structural and signaling defects in mechanically stressed tissue such as muscle and heart. (medscape.com)

Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation. (biomedcentral.com)
Our results provide a new resource to investigate transcription regulation in metazoans. (nih.gov)
Our results suggest that chromatin interactions may be a major mechanism by which transcription regulation occurs in human cells. (selectbiosciences.com)
However, it is now clear that chromatin structure is an integral part of the process of gene regulation. (nih.gov)
Predicted to be involved in regulation of transcription by RNA polymerase II. (nih.gov)
I am a molecular biologist by training with specialization in cancer research, mainly in transcription factor function and gene regulation in cancer. (helsinki.fi)
Recognition of acetylated chromatin marks by BRDs enables the regulation of gene expression through a wide range of activities. (frontiersin.org)
To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription factors to DNA. (nih.gov)
In addition to classical gene regulatory networks noted above, we have recently identified a central role for additional biologic mechanisms, namely gene regulation by chromatin regulators and by noncoding RNAs. (stanford.edu)
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)

Reverse transcription‑quantitative PCR was then used to validate the downstream targets. (spandidos-publications.com)
We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. (mendeley.com)

RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. (nih.gov)

The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin structure interact during normal erythropoiesis. (rochester.edu)
changes in the chromatin structure of a gene were considered to be the passive consequence of the binding of these factors. (nih.gov)
Their cell lineage-specific effects are governed by chromatin structure. (edu.au)
CBP has significant histone acetyltransferase activity and "opens" the chromatin structure so that transcription factors can enter and regulate gene expression. (medscape.com)

The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
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)

For chromatin modifications, they studied the combinatorial effect of histone modification and DNaseI hypersensitivity, producing good predictive power. (plantae.org)

We have identified a new motif, termed SMAD Complex Associated (SCA) that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. (ca.gov)
We demonstrate that two bHLH proteins - HEB and E2A - bind the SCA motif at regions overlapping SMAD2/3 and FOXH1. (ca.gov)
In occurs through the inhibition of DNA binding of cognate cis- hematopoiesis there exist several lineage branch points with regulatory motif while in the other case DNA binding is unaffected identified key transcription factors and external signals [3-5]. (lu.se)

Many distal transcription factor binding sites have been observed. (selectbiosciences.com)
Chromatin interactions can connect distal transcription factor binding sites with target gene promoters. (selectbiosciences.com)

Histone H3 is one of the DNA-binding proteins found in the chromatin of all eukaryotic cells. (fishersci.com)

Because rodents lack NLRP7, we used human embryonic stem cells to study its function and demonstrate that NLRP7 interacts with YY1, an important chromatin-binding factor. (nih.gov)
Our data demonstrate negative selection against binding sites alterations and suggest that such selection pressure protects cancer cells from rewiring of regulatory circuits. (biomedcentral.com)
By using "no signal" as an indication of closed chromatin, the low sample input from single cells is not problematic. (epigenie.com)
Their function is regulated by the activation of a number of activating and inhibitory receptors that bind to specific ligands expressed on the surface of target cells. (frontiersin.org)
Moreover, NK cells are poised to release cytokines such as IFN- γ , TNF-α and growth factors that can initiate inflammatory responses mediated by both the innate and the adaptive arm of the immune system. (frontiersin.org)

For SMiLE-seq, what the button captures is interactions between GFP-labeled transcription factors and a library of oligonucleotides. (genomeweb.com)
Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)

We previously observed MORC binding sites where RdDM does not occur (MORC-unique sites) [ 7 ], and by studying these sites, we aim to shed light on the mechanisms underlying the RdDM-independent functions of MORC proteins. (biomedcentral.com)

The topic of my lecture is skin epigenetics or the story on how chromatin regulators orchestrate skin functions. (hstalks.com)

Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. (nih.gov)

GATA3 regulates gene expression through binding nucleosomal DNA and facilitating chromatin remodelling. (bmj.com)

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. (nih.gov)
The lab's focus is transcriptional regulatory network inference, modeling gene expression as a function of transcription factor activities, from gene expression and measurements of chromatin state. (cincinnatichildrens.org)
Our method, which allowed us to map routinely temporal binding profiles of dozens of TFs, provides a foundation for future understanding of the mammalian regulatory code. (nih.gov)
Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. (lu.se)
Emerin is a ubiquitous inner nuclear membraneprotein, presentin nearly all cell types, although its highest expression is in skeletal and cardiacmuscle.Emerin binds to many nuclear proteins, including several gene-regulatory proteins (eg, barrier-to-autointegration factor, germ cell-less, Btf), nesprins (proteins that act as molecular scaffolds), F-actin, and lamins. (medscape.com)

they are also essential for DNA replication and mRNA transcription. (medscape.com)

We are currently investigating the function of chromatin modifiers during embryonic development, in adult stem cell populations and in cancer, and modelling chromatin-based intellectual disability to discover ameliorating treatments. (edu.au)

Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. (nih.gov)
This chromatin signature which consists of Smad transcription factors and both histone repressive and active marks is the most conducive for mediating downstream targets of Nodal, providing inroads into how signaling pathways and chromatin cooperate during fate specification in hESCs. (ca.gov)

As a principal investigator, I am leading the Enhancer Biology lab to understand the role of lineage-specific transcription factors and their collaboration with cancer-specific oncogenes in driving tumorigenesis. (helsinki.fi)

Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. (nih.gov)

In the case of transcription-factor based models, the authors describe that binding in the promoter region only has some predictive power in a few cases, showing that there is still work to do on this subject. (plantae.org)
Furthermore, it has been demonstrated that the binding of USF1 to the Chitinase 3-Like 1 (Chi3L1) promoter region can enhance the transcriptional activity of Chi3L1. (spandidos-publications.com)

In its binding with sulfhydryl groups, lead may interfere with the activity of zinc metalloenzymes, as zinc binds to a sulfhydryl group at the active site. (cdc.gov)

Currently, I am working on the role of lineage-specific trnascription factors in pancreatic ductal adenocarcinomas. (helsinki.fi)

Cancer somatic mutations in binding sites of selected transcription factors have been found under positive selection. (biomedcentral.com)
For many transcription factors, including multiple members of FOX, HOX, and NR families, we show that human cancers accumulate fewer mutations than expected by chance that increase or decrease affinity of predicted binding sites. (biomedcentral.com)

Assessment of potential binding affinity changes induced by substitutions allows studying selection of sequence variants in binding sites in a way resembling usage of non-synonymous and synonymous substitutions in codons. (biomedcentral.com)

This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. (nih.gov)
Upstream transcription factor (USF) 1 belongs to the basic helix-loop-helix leucine zipper family and serves as a cellular transcription factor (TF). (spandidos-publications.com)

Interestingly, recent data suggest a function for ULK1 not only during autophagy activation but also during elongation and closure of the autophagosomal membrane via binding to ATG8 proteins [ 8 ]. (hindawi.com)

We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. (elifesciences.org)

MORC-regulated transcription factors can in some cases regulate their own transcription, resulting in feedback loops. (biomedcentral.com)
One of the great missing pieces in our understanding of gene expression is how transcription factors regulate and control it in an orchestrated fashion. (genomeweb.com)

HEXIM1 is an Essential Transcription Regulator During Human Erythropoiesis. (rochester.edu)
A census of human transcription factors: function, expression and evolution. (nih.gov)

In N-ChIP, no fixing agent is used to crosslink proteins to the chromatin. (cellsignal.com)
Because antibodies are raised against unfixed antigens, N-ChIP offers the advantage of better recognition and binding of antibodies to their target antigens. (cellsignal.com)

Anatomy15

Organisms10

Chemicals and Drugs114

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Phenomena and Processes86

Disciplines and Occupations2

Information Science11

Health Care2

Immunoprecipitation9

Epigenetic11

Open chromatin1

Protein21

Assays4

Methylation14

Modulating chromatin structure1

Histones4

Genes15

Repressive chromatin marks1

Genome10

Signal transduction1

Genomic1

Accessibility4

Differentiation3

Interaction3

Conformation5

Motifs5

Functional1

Histone proteins1

Modifications and transcription factors1

Nucleus1

Regulation10

Quantitative2

Caenorhabditis1

Structure4

Genomes2

Combinatorial1

Motif3

Distal2

Eukaryotic1

Cells5

Interactions2

Mechanisms1

Regulators1

Signatures1

Regulates1

Regulatory5

Replication1

Embryonic1

Downstream2

Specific transcription factors1

Overlap1

Promoter region2

Zinc1

Lineage-specific1

Mutations2

Variants1

Basic helix2

Elongation1

Methyltransferase1

Regulate2

Human2

ChIP2