RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
The His-1 gene is developmentally expressed in the murine choroid plexus but is silenced in the adult brain. To test the hypothesis that the gene contains cis-acting elements that contribute to this repression, we have analyzed segments of the proximal promoter for negative regulatory sequences by transient transfection analysis. The activity of the proximal promoter was moderately influenced by positively and negatively acting sequences located from 2335 to 2168 and 2617 to 2335, respectively. A strong His-1-positive regulatory element (HPRE, 118 to 129) was essential for maximal promoter activity and could also enhance the activity of the heterologous SV40 promoter in an orientation-dependent manner. The HPRE contains homology to the neuronal restrictive silencer element (NRSE) but interacted with nuclear proteins that were distinct from the NRSE-binding factor (NRSF). By contrast, a potent negative regulatory sequence (HNRE) was identified in the first exon that repressed either the His-1 or ...
MOTIVATION Presently available programs for the recognition of potential transcription factor binding sites in genomic sequences generally yield a huge amount of output. These output lists have to be filtered to obtain biologically significant elements, which is highly laborious work to be done manually. RESULTS We developed a strategy for systematic verification and improvement of the underlying profiles, and for their contextual analysis by a fuzzy clustering approach using non-redundant libraries of search profiles as a prerequisite. AVAILABILITY The tools mentioned in the paper are available upon request. CONTACT [email protected]
Fingerprint Dive into the research topics of Multiple positive and negative 5 regulatory elements control the cell-type-specific expression of the embryonic skeletal myosin heavy-chain gene.. Together they form a unique fingerprint. ...
TY - JOUR. T1 - Use of MCF-7 cell variants to evaluate growth regulatory potential of estrogen-induced products. AU - Davidson, N. E.. AU - Bronzert, D. A.. AU - Chambon, P.. PY - 1985/1/1. Y1 - 1985/1/1. UR - http://www.scopus.com/inward/record.url?scp=17344375640&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=17344375640&partnerID=8YFLogxK. M3 - Article. AN - SCOPUS:17344375640. VL - VOL. 26. SP - No. 777. JO - Proceedings of the American Association for Cancer Research. JF - Proceedings of the American Association for Cancer Research. ER - ...
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A number of interactive questions are embedded within the short film The Making of the Fittest: Evolving Switches, Evolving Bodies, which illustrates how mutations in gene regulatory regions can result in the evolution of major anatomical features.. ...
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The regulation of transcription requires complex interactions between proteins bound to DNA sequences that are often separated by hundreds of base pairs. As demonstrated by a nuclear ligation assay, the distal enhancer and the proximal promoter regions of the rat prolactin gene were found to be juxtaposed. By acting through its receptor bound to the distal enhancer, estrogen stimulated the interaction between the distal and proximal regulatory regions two- to threefold compared to control values. Thus, the chromatin structure of the prolactin gene may facilitate the occurrence of protein-protein interactions between transcription factors bound to widely separated regulatory elements. ...
Transcriptional repressor required to restrict transcription of ECB-dependent genes to the G1/M phase by repressing their transcription during the interval from late G1 to M phases. Genes that contain a ECB (early cell box) element in their transcription regulatory region are transcribed only during G1/M phases. In vitro, is capable of binding to the DNA of the leucine tRNA gene.
Tomás Allen Rush, Virginie Puech-Pagès, Adeline Bascaules, Patricia Jargeat, Fabienne Maillet, Alexandra Haouy, Arthur QuyManh Maës, Cristobal Carrera Carriel, Devanshi Khokhani, Michelle Keller-Pearson, Joanna Tannous, Kevin R. Cope, Kevin Garcia, Junko Maeda, Chad Johnson, Bailey Kleven, Quanita J. Choudhury, Jessy Labbé, Candice Swift, Michelle A. OMalley, Jin Woo Bok, Sylvain Cottaz, Sébastien Fort, Verena Poinsot, Michael R. Sussman, Corinne Lefort, Jeniel Nett, Nancy P. Keller, Guillaume Bécard, Jean-Michel ...
Cells use protein-DNA and protein-protein interactions to regulate transcription. A biophysical understanding of this process has, however, been limited by the lack of methods for quantitatively characterizing the interactions that occur at specific promoters and enhancers in living cells. Here we show how such biophysical information can be revealed by a simple experiment in which a library of partially mutated regulatory sequences are partitioned according to their in vivo transcriptional activities and then sequenced en masse. Computational analysis of the sequence data produced by this experiment can provide precise quantitative information about how the regulatory proteins at a specific arrangement of binding sites work together to regulate transcription. This ability to reliably extract precise information about regulatory biophysics in the face of experimental noise is made possible by a recently identified relationship between likelihood and mutual information. Applying our experimental ...
histone deacetylase complex, nucleoplasm, nucleus, DNA-binding transcription factor activity, DNA-binding transcription factor activity, RNA polymerase II-specific, transcription factor binding, transcription regulatory region sequence-specific DNA binding
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity are frequently unreliable. On the other hand, comprehensive experimental validation is difficult and time consuming. We introduce a simple strategy that dramatically improves robustness and accuracy of computational binding site prediction. First, we evaluate the rate of recurrence of computational TFBS predictions by commonly used sampling procedures. We find that the vast majority of results are biologically meaningless. However clustering results based on nucleotide position improves predictive power. Additionally, we find that positional clustering increases robustness to long or imperfectly selected input sequences. Positional clustering can also be used as a mechanism to integrate results from multiple sampling approaches for improvements in accuracy over each one ...
Multiple cis-acting sequences contribute to evolved regulatory variation forDrosophila Adh genes. Delineation of cis-acting sequences required for expression of Drosophila mojavensis Adh-1
Cis-regulatory modules (CRM) are segments of DNA responsible for tissue- and time- specific regulation of gene expression (1). The length of CRMs is difficult to estimate directly but it is believed to vary from several hundreds to several thousands of ba
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Science 8 May 2015: Vol. 348 no. 6235 pp. 618-619 New database links regulatory DNA to its target genes. Elizabeth Pennisi. [paraphrase]. Several major research consortia have delivered what amount to users manuals for the genome, mapping the locations of thousands of regulatory genomic switches, the specific genes they control, and where in the body they are turned on or off. The latest and arguably boldest of the big biology efforts has yielded preliminary results. By analyzing genetic material gleaned from more than 100 people who had died just hours before, the Genotype-Tissue Expression (GTEx) project portrays gene regulation in action, identifying the genes switched on or off by subtle changes in DNA within 2 million bases of any gene. By evaluating multiple tissues from each body, it also charts the reach of those regulatory sequences across cell types some affect a gene in all tissues; others are influential in a few tissues or just one. Earlier efforts took other approaches to mapping ...
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1. MEET.5.1:Motif Element Estimation Tools - MEET 5.1 is an R-package that includes a set of models, aprox. 550, and tools for the detection of cis-regulatory sequences ...
Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription, DNA-templated; response to cold; and sleep. Predicted to localize to nucleus. Is expressed in several structures, including brain; cardinal system; pleuroperitoneal region; shield; and swim bladder bud. Orthologous to human BHLHE41 (basic helix-loop-helix family member e41 ...
Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in otic placode formation. Predicted to localize to nucleus. Is expressed in several structures, including fin bud; germ ring; immature eye; median fin fold; and nervous system ...
The hINV basal promoter, which encodes forty one nucleotides upstream of the transcription commence web site and no AP1 web sites, is not controlled by TAM67
Looking for online definition of Regulatory elements in the Medical Dictionary? Regulatory elements explanation free. What is Regulatory elements? Meaning of Regulatory elements medical term. What does Regulatory elements mean?
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The Details by cell line view is the default view, where you get the generic MultiCell regulatory feature and cell-specific classifications, as well as part of their supporting evidence displayed as tracks. To display more evidence tracks, you can go to the Configure this page link and select tracks within the Regulation subsection. DNA Methylation and external sources (Other regulatory regions) are not used as evidence for regulatory regions ...
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Since the sequencing of the human genome in 2001, all our genes - around 20,000 in total - have been identified. But much is still unknown - for instance where and when each is active. Next to each gene sits a short ...
A Consumer Guide discusses the basic technical, economic and regulatory information you should know before buying a photovoltaic (PV) solar electric generation system.
Newly developed genome-editing tools, such as the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, allow simple and rapid genetic modification in most model organisms and human cell lines. Here, we report the production and analysis of mice carrying the inactivation via deletion of a genomic insulator, a key non-coding regulatory DNA element found 5′ upstream of the mouse tyrosinase (Tyr) gene. Targeting sequences flanking this boundary in mouse fertilized eggs resulted in the efficient deletion or inversion of large intervening DNA fragments delineated by the RNA guides. The resulting genome-edited mice showed a dramatic decrease in Tyr gene expression as inferred from the evident decrease of coat pigmentation, thus supporting the functionality of this boundary sequence in vivo, at the endogenous locus. Several potential off-targets bearing sequence similarity with each of the two RNA guides used were analyzed and found to be largely intact. This study reports ...
Previous work has suggested that the promoter regions of the human embryonic zeta 2 and epsilon globin genes contain negative regulatory regions that could play a role in the repression of these genes in postembryonic erythroblasts. We have examined this possibility by studying the expression of these genes in mouse erythroleukemia cells, an adult erythroid cell line that might be expected to contain repressor molecules that would bind to the putative negative regulatory regions. When attached to appropriate upstream regulatory elements (alpha HS-40 and beta HS1,2) both the zeta and epsilon genes were expressed in these cells at a low level, but no increase in expression was observed when similar constructs lacking the proposed negative regulatory sequences were introduced into these cells. These results cast doubt on the possibility that these sequences play a major role in the developmental repression of the embryonic globin genes, unless they function only in a normal chromosomal organization.
TRANSFAC 3.2 is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzolds SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several ...
Enhancers and promoters are cis-acting regulatory elements associated with lineage-specific gene expression. Previous studies showed that different categories of active regulatory elements are in regions of open chromatin, and each category is associated with a specific subset of post-translationally marked histones. These regulatory elements are systematically activated and repressed to promote commitment of hematopoietic stem cells along separate differentiation paths, including the closely related erythrocyte (ERY) and megakaryocyte (MK) lineages. However, the order in which these decisions are made remains unclear. To characterize the order of cell fate decisions during hematopoiesis, we collected primary cells from mouse bone marrow and isolated 10 hematopoietic populations to generate transcriptomes and genome-wide maps of chromatin accessibility and histone H3 acetylated at lysine 27 binding (H3K27ac). Principle component analysis of transcriptional and open chromatin profiles demonstrated that
Mammalian transcription is controlled by a complex interplay of regulatory events. Together, these events determine the correct spatio-temporal initiation and rate of RNA polymerase II (RNAPII) gene transcription. Several decades of research on transcriptional regulation have identified different modes of regulation that have been ascribed to distinct regulatory elements - stretches of DNA with specific…
Ng, C. [伍志祥。]. (1999). Identification of cis-regulatory sequence for the expression of epidermal growth factor (EGF) gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_ ...
IDT facilitates a unique, scalable method for analyzing hundreds of enhancer:promoter interactions in a single assay Advancing the development of novel methods for understanding gene expression, Integrated DNA Technologies (IDT) has enabled Dr Jim Hughes, Associate Professor at the Weatherall Institute of Molecular Medicine, Oxford, UK, to optimize his unique Capture-C method, based on Chromosomal Conformational Capture (3C). As outlined in the recent DECODED Online article, Understanding How Distal Regulatory Elements Control Gene...
The systematic prediction and categorisation of promoters, repressors, enhancers, etc., is not only essential to unravel the inner workings of biochemical networks, but also to engineer novel synthetic ones. Each putative regulatory region, however, has to be validated experimentally in order to be categorized as a fully defined functional element, which constitutes a significant bottleneck. In most studies, the promoter activity is illustrated as the amount of fluorescence divided by the optical density. These values are obtained from a coupled time-series experiment. With relatively simple mathematical reasoning, a tool that describes promoter activity in each time point has been implemented. The protein expression and the protein maturation process are modelled as a first order differential equations taking into account the degradation and the maturation rates which are to be known in advance. The promoter activity is then expressed based on the measured quantities of optical density and ...
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Assume we have a set of sequences upstream of genes that are involved in a pathway with a common function. Since these genes are to be regulated more or less simultaneously, common regulatory factors or CIS-acting elements are likely to be involved. We want to investigate if, among the set of sequences, certain motifs are responsible for the regulation. An indication for this would be if we can find motifs that are present very frequently.
ENCODES a protein that exhibits dynein complex binding (ortholog); transcription regulatory region DNA binding (ortholog); INVOLVED IN motile cilium assembly (ortholog); positive regulation of gene expression (ortholog); positive regulation of non-motile cilium assembly (ortholog); ASSOCIATED WITH Giant Axonal Neuropathy (ortholog); FOUND IN nuclear body (ortholog); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cobalt dichloride
The valve acts similar to one on a Basketball or Volleyball! On TV she won an Emmy for her 1975 TV Special Gypsy in My Soul and gave a well-publicized star turn on the 2012/2013 season of PBS Downton Abby. Three review authors independently extracted data using a standard form and assessed study quality! The level of expression of a gene encoding a particular revTetR protein may be manipulated by the choice of promoters with different transcription rates to which the revTetR coding sequence is operably associated, the inclusion of one or more positive and/or negative regulatory sequences which control the rate of transcription from that promoter, and the copy number of the vector carrying the revTetR coding sequence. Im using the same blog platform as yours and Im having difficulty finding one? Niel uptown differin gel over the counter canada has broken his arm, but all he cares about is the beauty of the Forresters house and the smell of Mrs. You can also explore some of this yourself ...
Corine Bertolotto, Roser Buscà, Patricia Abbe, Karine Bille, Edith Aberdam, et al.. Different cis -Acting Elements Are Involved in the Regulation of TRP1 and TRP2 Promoter Activities by Cyclic AMP: Pivotal Role of M Boxes (GTCATGTGCT) and of Microphthalmia. Molecular and Cellular Biology, American Society for Microbiology, 1998, 18 (2), pp.694-702. ⟨10.1128/mcb.18.2.694⟩. ⟨inserm-02533084⟩ ...
It is known that lamin A interacts with a variety of nuclear factors, including transcriptional regulators, chromatin, and nuclear membrane associated proteins. However it still remains unclear which proteins, genes, or regulatory DNA elements interact with lamin A in normal cells,or with progerin and lamin A in HGPS cells. We hypothesize that perturbations of chromatin structure and nuclear organization by progerin result in genome-wide defects in gene transcription, ultimatelyleading to HGPS. To test this idea, our approach combines chromatin immunoprecipitation, Hi-C approach of mapping of high-order nuclear organization, with next-generation sequencing and/or mass spectrometry techniques. Our goal is to identify differentially modified chromatin regions and differentially associated protein/DNA elements with lamin A and progerin in HGPS cells. Combined with gene expression analysis, we also aim to develop novel methods to integrate those multi-dimensional genomic data with gene expression ...
The temporally and spatially restricted expression of the mouse Engrailed (En) genes is essential for development of the midbrain and cerebellum. The regulation of En-2 expression was studied using in vitro protein-DNA binding assays and in vivo expression analysis in transgenic mice to gain insight into the genetic events that lead to regionalization of the developing brain. A minimum En-2 1.0 kb enhancer fragment was defined and found to contain multiple positive and negative regulatory elements that function in concert to establish the early embryonic mid-hindbrain expression. Furthermore, the mid-hindbrain regulatory sequences were shown to be structurally and functionally conserved in humans. The mouse paired-box-containing genes Pax-2, Pax-5 and Pax-8 show overlapping expression with the En genes in the developing brain. Significantly, two DNA-binding sites for Pax-2, Pax-5 and Pax-8 proteins were identified in the 1.0 kb En-2 regulatory sequences, and mutation of the binding sites ...
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One of the primary goals in the field of genetics is to identify genetic variants that contribute to disease heritability. Elucidating the functional consequence of genetic variants associated with disease provides essential insights into the molecular mechanisms that define human traits. However, this is complicated by the fact that a preponderance of disease-associated genetic variation lies outside of protein-coding genes. Rather than modify protein structure and function, these noncoding variants frequently impact regulatory elements and thereby alter the quantitative and spatiotemporal regulation of gene expression.. The regulation of gene expression is critical for establishing and maintaining the diverse cell types of the human body. Genes with critical cellular functions are frequently regulated through a circuit involving multiple regulatory elements that are brought within physical proximity by DNA folding. These complex regulatory circuits are hotspots for genetic predisposition to ...
Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or
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The xmlToEdit element is an optional element of the editing element.. xmlToEdit elements are used to define the editing components that can be used in a form. The xmlToEdit elements can contain multiple editWith elements that specify the editing components that will be used to edit various types of XML DOM nodes.. ...
Product Technical Documentation containing information regarding composition, manufacturing process, analyses and regulatory information useful for the label of the finished product ...
The Comedy Conglomerate is a student organization founded in Fall 2018 focused on comedy and creative media. You can find their work on Instagram, Youtube, and Facebook. Sam Frye, the founding member and presid...