• We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. (nih.gov)
  • They serve as bridges between transcriptional regulation and phenotypic variation in mammals. (nature.com)
  • Accordingly, three-dimensional genome architecture models at various resolutions, based on chromatin interactomes, have provided a conceptual framework for transcriptional regulation in animals ranging from flies to humans 12 . (nature.com)
  • However, due to the limited resolution of Hi-C maps, comprehensive high-resolution chromatin maps involving regulatory elements, which allow for elucidation of their impact on transcriptional regulation are still lacking in plants. (nature.com)
  • Essentiality of the Maltase AmlE in Maltose Utilization and Its Transcriptional Regulation by the Repressor AmlR in the Acarbose-Producing Bacterium Actinoplanes sp. (frontiersin.org)
  • Their regulation may be carried out either through direct binding to DNA as peroxisome proliferator-activated receptors or via modulation in an indirect manner of signaling pathway molecules (e.g., protein kinase C) and other transcription factors (nuclear factor kappa B and sterol regulatory element binding protein). (springer.com)
  • The differential regulation of aos and btd domains by dri occurs at a time when Dri is found in all somatic nuclei of the embryo, so that Dri must be acting to permit the proper function of other developmental regulatory factors. (sdbonline.org)
  • Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. (aps.org)
  • To that end, we present a theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model which applies to a variety of regulatory architectures. (aps.org)
  • Research efforts to date have focused on identifying how either components of the phosphoenolpyruvate-phosphotransferase system (PTS) or global transcriptional networks affect the regulation of virulence factors, but not the synergistic relationship between the two. (umd.edu)
  • The lab is also characterizing members of a novel THAP domain protein family regarding their roles in gene regulation, chromatin signaling, cell growth and differentiation and cancer. (northwestern.edu)
  • Transcriptional regulation information for a gene, including any predicted DNA binding site motifs ( YeTFaSCo ) for the gene's protein product, as well as any of its targets (genes it regulates) or regulators (genes that regulate it), based on experimental evidence. (yeastgenome.org)
  • Singh, R.P., Prasad, H.K., Sinha, I., Agarwal, N. and Natarajan, K. (2011) Cap2-HAP Complex Is a Critical Transcriptional Regulator That Has Dual but Contrasting Roles in Regulation of Iron Homeostasis in Candida albicans. (jnu.ac.in)
  • adequately represent genomic regulation for diagnosis and Historically, it has been within the domain of signal therapy. (lu.se)
  • 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)
  • Activation of Btk results in a cascade of signaling events resulting in calcium mobilization and fluxes, cytoskeletal rearrangements, and transcriptional regulation involving nuclear factor-kappaB (NF-kappaB) and nuclear factor of activated T cells (NFAT). (medscape.com)
  • Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
  • (C) Wire diagram (BioTapestry) showing the complex regulatory network between the four MADS proteins themselves. (frontiersin.org)
  • One of Chakravarti's major research interests is to determine the mechanisms of steroid hormone and vitamin signaling with special emphasis on the role of the nuclear hormone receptor co-regulatory proteins in gene transcription. (northwestern.edu)
  • We, in a dogma changing study demonstrated that key cell cycle genes are regulated by HCFC1 cofactor recruitment not by the E2F proteins but by a THAP11-ZNF143 transcriptional complex. (northwestern.edu)
  • Secondly, our effort will stimulate future research on further characterization of all THAP domain proteins. (northwestern.edu)
  • The Phactr family of PP1-binding proteins and the myocardin-related transcription factor family of transcriptional coactivators contain regulatory domains comprising three copies of the RPEL motif, a G-actin binding element. (rcsb.org)
  • This entry represents the N-terminal domain of PhnA proteins, which is predicted to form a zinc-ribbon, found in some proteobacteria. (embl-heidelberg.de)
  • There are 391 PhnA_Zn_Ribbon domains in 391 proteins in SMART's nrdb database. (embl-heidelberg.de)
  • Taxonomic distribution of proteins containing PhnA_Zn_Ribbon domain. (embl-heidelberg.de)
  • The complete taxonomic breakdown of all proteins with PhnA_Zn_Ribbon domain is also avaliable . (embl-heidelberg.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing PhnA_Zn_Ribbon domain in the selected taxonomic class. (embl-heidelberg.de)
  • Candidates for other membrane components and regulatory proteins are also identified. (embl-heidelberg.de)
  • Evolutionary alignment of Twist proteins from different species, indicate TWIST contain 4 additional conserved regions such as NSEEE, NLS1, NLS2, and WR-domain besides the bHLH motif. (uni-marburg.de)
  • The bHLH domain is thought to be responsible for heterodimerization with other bHLH proteins such as E12 protein or SEF2 protein. (uni-marburg.de)
  • I wanted to determine if the TWIST protein or its conserved motifs interact with other regulatory proteins to help to regulate the TWIST transcriptional activity. (uni-marburg.de)
  • Furthermore, two more highly conserved TWIST motifs NSEEE and WR were analyzed individually to find out their interacting proteins and their role in regulating the TWIST1 transcriptional activity. (uni-marburg.de)
  • It probably projects out of the globular catalytic domain and may interact with the acidic activator domains of transcriptional regulatory proteins. (embl.de)
  • Transcription is regulated through the binding of transcription factor proteins to specific cis -level regulatory sites in the DNA. (ucsc.edu)
  • For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. (ucsc.edu)
  • Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. (bvsalud.org)
  • 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)
  • His studies have revealed a repertoire of highly dynamic transcriptional regulatory sequences as well as transcriptional regulators that are previously uncharacterized. (chop.edu)
  • By integrating expression quantitative trait locus (eQTL) and genome-wide association study (GWAS) data, we demonstrate that long-range chromatin interactions between variant regulatory elements and their target genes contribute to variations in gene expression, metabolic phenotypes, and agronomic traits. (nature.com)
  • MATERIALS & METHODS: Microarray DNA methylation data were analyzed and associated with functional/regulatory genome annotation data, transcriptional profiles and clinicobiological parameters. (ca.gov)
  • The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements. (biomedcentral.com)
  • Signals generated by the genome must be processed to the genome, regulatory models require the kind of nonlinear characterize their regulatory effects and their relationship to dynamics studied in signal processing and control. (lu.se)
  • Tiling a given promoter region with several sgRNAs can produce more robust transcriptional activation 9 - 11 , but this requirement presents enormous challenges for scalability, and in particular for establishing pooled, genome-wide GOF screens. (cdc.gov)
  • in an operon with an upstream PurR/LacI-type transcriptional regulator gene, named amlR ( ACSP50_2475 ), and a gene downstream ( ACSP50_2473 ) encoding a GGDEF-EAL-domain-containing protein putatively involved in c-di-GMP signaling. (frontiersin.org)
  • Although AmlR apparently is a local transcriptional regulator of the aml operon, the Δ amlR strain shows severe growth inhibitions on glucose and - concomitantly - differential transcription of several genes of various functional classes. (frontiersin.org)
  • Here we report DBC1 as a key regulator of AR-V7 transcriptional activity and stability in CRPC cells. (cancerindex.org)
  • While it is known that the PTS can affect activity of the Mga virulence regulator, further characterization of the mechanism by which sugars and its protein domains affect activity have not been studied. (umd.edu)
  • Transcriptional Profiling Shows that Gcn4p is a Master Regulator of Gene Expression During Amino Acid Starvation in Yeast. (jnu.ac.in)
  • ERK-mediated S98 phosphorylation inhibits assembly of G-actin complexes on the MRTF-A regulatory RPEL domain, promoting nuclear import. (elifesciences.org)
  • Sinha I, Poonia P, Sawhney S, Natarajan K. (2017) Functional Specialization of Two Paralogous TAF12 Variants by Their Selective Association with SAGA and TFIID Transcriptional Regulatory Complexes. (jnu.ac.in)
  • We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)
  • RESULTS: DNA methylation changes in neuroblastoma affect not only promoters but also intragenic and intergenic regions at cytosine-phosphate-guanine (CpG) and non-CpG sites, and target functional chromatin domains of development and cancer-related genes such as CCND1. (ca.gov)
  • To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation. (bvsalud.org)
  • High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). (bvsalud.org)
  • Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. (bvsalud.org)
  • The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. (scielo.br)
  • Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. (nature.com)
  • In eukaryotes, cis regulatory elements and associated trans -acting factors regulate spatiotemporal gene expression, which affects individual development. (nature.com)
  • This chromatin organization differentially instructed alternative Abd-B promoter use, thereby expanding the possibilities to regulate transcriptional output. (biorxiv.org)
  • In addition, phosphorylation of a serine in a conserved short stretch within an acidic domain of T. reesei CRE1 has been demonstrated to regulate its DNA binding [ 13 ]. (biomedcentral.com)
  • MADS domain transcription factors are key regulators in yeast, animals, and plants. (frontiersin.org)
  • These different actions must depend on the combination of regulators acting on the respective position-specific cis-regulatory sequences. (sdbonline.org)
  • Additional studies are underway to experimentally test novel regulatory DNA sequences and transcriptional regulators. (chop.edu)
  • RESULTS: In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. (bvsalud.org)
  • First, I focused on functional characterization of the NLS1 and NLS2 domains as potential nuclear localization signals in TWIST. (uni-marburg.de)
  • The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. (biomedcentral.com)
  • Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. (bvsalud.org)
  • Most peaks, clearly enriched for CArG-box sequences, are present in upstream promoter regions close to the transcriptional start site, though some are also found in introns and 3′-UTR regions. (frontiersin.org)
  • Priyadarshini Y., Natarajan, K. (2016) Reconfiguration of transcriptional control of lysine biosynthesis in Candida albicans involves a central role for the Gcn4 transcriptional activator. (jnu.ac.in)
  • Background: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. (researchgate.net)
  • He is also developing computational algorithms for constructing models of transcriptional regulatory and signaling networks by integrating multi-dimensional genomic, epigenomic, and transcriptomic datasets. (chop.edu)
  • Dr. Tan is developing cutting-edge genomic and computational tools to profile and model the gene regulatory circuitry in these two developmental systems. (chop.edu)
  • We describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. (cdc.gov)
  • In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. (biomedcentral.com)
  • Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research. (bvsalud.org)
  • Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. (plos.org)
  • CpG sites located in the promoter region are usually not methylated, while CpG outside the regulatory region of genes is methylated. (creativebiomart.net)
  • Moreover, DNA hypermethylation can also occur during the development of cancer, especially in CpG islands of the promoter region, resulting in transcriptional silencing of affected genes, such as tumor suppressor genes. (creativebiomart.net)
  • The elevated expression of p53 leads to greater stability, which also induces the regulatory protein Mdm2. (shu.edu)
  • Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). (nature.com)
  • The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. (nature.com)
  • In this study, we explore the regulatory role of mutations occurring in distal regulatory elements related to gene expression and phenotypic variations with adapted long-read ChIA-PET, and construct high-resolution chromatin interaction maps of maize promoter proximal regions and distal regulatory elements associated with RNA polymerase II occupancy and histone mark H3K4me3. (nature.com)
  • and c) the C-terminal DNA-binding domain, ETS, which binds to the consensus DNA sequence, 5-GGAA/T-3 within a 9-to-10 bp sequence, in the target genes it regulates. (wikipedia.org)
  • Early studies showed that FinO specifically binds the 3' transcriptional terminator structure of FinP in a manner that critically relies on both the GC-rich hairpin and 3' polypyrimidine tail that define the terminator 16 , and further work showed that the base of the hairpin and 3' tail are both strongly protected from ribonuclease degradation by FinO 17 . (nature.com)
  • Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. (scielo.br)
  • In this disturbance the maintenance involve the gene expression under the stress either in the form of structural gene or regulatory. (scielo.br)
  • Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
  • Hence, TADs are believed to represent structural chromosomal units that are of functional importance for the regulatory cross talk that determines gene expression programs. (biomedcentral.com)
  • Overall, the studies presented sought to define how external environmental cues, specifically carbohydrates, control complex regulatory networks used by GAS, contribute to pathogenesis, and aid in adaptation to various nutrient conditions encountered. (umd.edu)
  • This gene encodes for a bHLH transcription factor, which inhibits osteogenic differentiation by transcriptional control of various target genes. (uni-marburg.de)
  • For example, engineered RNAs can be used as switches to interface with protein-based transcriptional control via CRISPR/Cas systems. (unm.edu)
  • Since requires its own model systems, not simply straightforward transcriptional (and posttranscriptional) control involves the adaptations of currently formulated models. (lu.se)
  • We suggest that these 5' CpG domains are required to distort the chromatin structure and to increase gene activity. (nih.gov)
  • These mutations are typically seen in the DNA binding domain, which affects transcriptional activity and its overall cellular activities. (shu.edu)
  • Pentapeptide insertion mutagenesis of the Hoxa1 protein: mapping of transcription activation and DNA-binding regulatory domains. (nih.gov)
  • This activation correlates with the differential phosphorylation of Mga at its PTS regulatory domains (PRDs). (umd.edu)
  • In Drosophila , the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive replacement of histone modifications, reorganization of 3D chromatin architecture and sequential activation of boundary elements and cis -regulatory regions. (biorxiv.org)
  • The collinear activation of the Hox genes and their cis -regulatory elements is thought to rely on the progressive opening of the chromatin within the BX-C along the A-P axis. (biorxiv.org)
  • We map multiple sites of serum-induced phosphorylation, most of which are S/T-P motifs, and show that S/T-P phosphorylation is required for transcriptional activation. (elifesciences.org)
  • TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy to promote transcriptional activation. (jnu.ac.in)
  • 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)
  • A transcription factor that possesses DNA-binding and E2F-binding domains but lacks a transcriptional activation domain. (bvsalud.org)
  • Transcriptional studies revealed that the core Mga regulon is activated more in a glucose-rich than a glucose-poor environment. (umd.edu)
  • Our work establishes the importance of the Fab-7 boundary element for insulation between 3D domains marked by different histone modifications. (biorxiv.org)
  • Interestingly, we detected a non-canonical inversion of collinear chromatin dynamics at the Abd-B gene, with the active histone domain decreasing in size. (biorxiv.org)
  • The aim of my work is to characterize functional domains in TWIST protein, and to determine the interacting partner for TWIST and its motifs particularly NSEEE and WR. (uni-marburg.de)
  • We work on prototyping novel genetic regulatory motifs in cell-free transcription/translation systems and on realizing these in living cells and in synthetic cells. (unm.edu)
  • The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. (bvsalud.org)
  • Three G-actins surround the crank-shaped RPEL domain forming a closed helical assembly. (rcsb.org)
  • Their spatial relationship is identical to the RPEL-actins within the pentavalent MRTF G-actin⋅RPEL domain complex, suggesting that conserved cooperative interactions between actin⋅RPEL units organize the assembly. (rcsb.org)
  • His laboratory is using the integrative approach to dissect the gene regulatory networks controlling embryonic hematopoiesis, T cell differentiation, and oncogenesis. (chop.edu)
  • However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. (nature.com)
  • To exert stimulatory or repressive effects on transcription, accessible regulatory DNA elements must be in close spatial proximity to susceptible genes. (biomedcentral.com)
  • Engineering biological systems involves creating abstractions that can be formalized as domain-specific modeling languages. (unm.edu)
  • Likewise, the ProQ/FinO domain-containing protein RocC of Legionella pneumophila interacts with only one trans -acting sRNA (RocR) to repress post-transcriptionally multiple mRNA targets 6 . (nature.com)
  • For genes with regulatory targets, shared GO Biological Process terms for these targets are listed. (yeastgenome.org)
  • This table lists putative transcriptional regulatory targets for the central gene represented on this page. (yeastgenome.org)
  • Our results highlight the significance of 3D organization of regulatory elements and suggest that the topology of long-range genetic variations may affect gene expression as well as phenotype variation. (nature.com)
  • Two unrelated kindreds were found to have autosomal dominant inherited mutations in the ETV6 gene, one family with a germline DNA substitution termed L349P that lead to replacing leucine with proline at amino acid 349 in the DNA binding domain of the ETV6, the second, termed N385fs, in germline DNA caused the lose of five base pairs ETV6 and a truncated ETV6 protein. (wikipedia.org)
  • However, our understanding of the regulatory mechanisms of AR-V7-driven transcription is limited. (cancerindex.org)
  • Here we show that bivalent domains and chromosome architecture for bivalent genes are dynamically regulated during the cell cycle in human pluripotent cells. (researchgate.net)
  • CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. (nih.gov)
  • Constitutively active AR-V7, one of the major androgen receptor (AR) splice variants lacking the ligand-binding domain, plays a key role in the development of castration-resistant prostate cancer (CRPC) and anti-androgen resistance. (cancerindex.org)
  • It contains paired amphipathic helix (PAH) domains, which are important for protein-protein interactions and may mediate repression by the Mad-Max complex. (antikoerper-online.de)
  • Homomeric interactions of the MPZ Ig domain and their relation to Charcot-Marie-Tooth disease. (medscape.com)
  • Chromatin loops connect regulatory elements to their target genes. (nature.com)