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 ...
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. ...
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.
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
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 ...
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 ...
nucleus, DNA-binding transcription factor activity, sequence-specific DNA binding, transcription regulatory region DNA binding, cell differentiation, regulation of transcription, DNA-templated, seed trichome elongation
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?
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.
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.
... 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 ...
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 ...
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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
aacggccaca agttcagcgt 3660gtccggcgag ggcgagggcg atgccaccta cggcaagctg accctgaagt tcatctgcac 3720caccggcaag ctgcccgtgc cctggcccac cctcgtgacc accctgacct acggcgtgca 3780gtgcttcagc cgctaccccg accacatgaa gcagcacgac ttcttcaagt ccgccatgcc 3840cgaaggctac gtccaggagc gcaccatctt cttcaaggac gacggcaact acaagacccg 3900cgccgaggtg aagttcgagg gcgacaccct ggtgaaccgc atcgagctga agggcatcga 3960cttcaaggag gacggcaaca tcctggggca caagctggag tacaactaca acagccacaa 4020cgtctatatc atggccgaca agcagaagaa cggcatcaag gtgaacttca agatccgcca 4080caacatcgag gacggcagcg tgcagctcgc cgaccactac cagcagaaca cccccatcgg 4140cgacggcccc gtgctgctgc ccgacaacca ctacctgagc acccagtccg ccctgagcaa 4200agaccccaac gagaagcgcg atcacatggt cctgctggag ttcgtgaccg ccgccgggat 4260cactctcggc atggacgagc tgtacaagta aagcggccgc gactctagat cataatcagc 4320cataccacat ttgtagaggt tttacttgct ttaaaaaacc tcccacacct ccccctgaac 4380ctgaaacata aaatgaatgc aattgttgtt gttaacttgt ttattgcagc ttataatggt 4440tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc actgcattct ...
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.. ...
Author Summary The spatial-temporal expression pattern of a gene, which is crucial to its function, is controlled by cis-regulatory DNA sequences. Forming the basic units of regulatory sequences are transcription factor binding sites, often organized into larger modules that determine gene expression in response to combinatorial environmental signals. Understanding the conservation and change of regulatory sequences is critical to our knowledge of the unity as well as diversity of animal development and phenotypes. In this paper, we study the evolution of sequences involved in the regulation of body patterning in the Drosophila embryo. We find that mutations of nucleotides within a binding site are constrained by evolutionary forces to preserve the sites binding affinity to the cognate transcription factor. Functional binding sites are frequently destroyed during evolution and the rate of loss across evolutionary spans is roughly constant. We also find that the evolutionary fate of a site strongly
Predicted to have activating transcription factor binding activity; protein C-terminus binding activity; and transcription regulatory region DNA binding activity. Involved in negative regulation of transcription, DNA-templated and response to interferon-gamma. Predicted to localize to the PML body; cell surface; and cytosol. Used to study MHC class II deficiency and osteoporosis. Human ortholog(s) of this gene implicated in Addisons disease; MHC class II deficiency; autoimmune hypersensitivity disease (multiple); myocardial infarction; and rheumatoid arthritis (multiple). Is expressed in bladder; central nervous system; and retina. Orthologous to human CIITA (class II major histocompatibility complex transactivator ...
While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed
The genome has intricate controls of its function, usually in a highly quantitative, coordinated and dynamic manner. Studies of genetics usually focused on how bases (A/T/C/G) lead to a function, or binary presence of absence of genes or regulatory elements for controlling its function, rather than seeking for a comprehensive dynamic and quantitative picture. For example, it remains major questions how quantitative gene expression leads to different functions, or how multiple regulatory elements (e.g., enhancers) work together to control diverse outcomes of the genome (considering it is the same DNA sequence). Driven by curiosity and availability of new tools, we aim to apply genetic engineering and other high-throughput perturbation and measure methods to study how genes and regulatory elements quantitatively contributes to the overall function fo the genome. We are also very interested in exploring how epigenetics (chemical modifcations of the DNA or nucleosomes) modulate and affect the ...
For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to ...
Data on 6,500 pesticides, insecticides and herbicides including toxicity, water pollution, ecological toxicity, uses and regulatory status.
Data on 6,500 pesticides, insecticides and herbicides including toxicity, water pollution, ecological toxicity, uses and regulatory status.
Sulphate is a macro element known to be beneficial to calcification of the coral skeletal matrix and health of SPS/LPS coral, when used in conjunction with Triton Lab ICP testing for appropriate dosing
Expression of GSDMB (GSDML, PRO2521) in human tissue. Overview of the antibody staining with HPA023925, HPA052407 and CAB013681 in immunohistochemistry
51900DNAZea mays 1atcgtaatcg gttttcaccg tataccgaac cgaaaaaacc gaataccaaa ctttatcaat 60tcccaaattt gactattcga ttatgtgaac taattgtgtg atacaattaa attgttattc 120acttatttgt atgtgatgta tgatgtatat ctaaatattt gtacctatat aatttttact 180ttttaaaatt atatgtaatc tatcatgtaa acttgttgta tgtattgtct tgattataag 240tttggtattc ggtttttacc gaaaaatcga agtaaaaaac cgaaaccgaa cttctcggtt 300tttcattttc tagaaaaccg aacggtttct aatgtttgaa aaaccgaagt tttttaaaac 360cgaaaaaccg aaccgaagtt tagaaaaaaa ccgaatgccc agccctaaaa attagtaccc 420cataagaact aaaaaaagat aaaatgacta aaaattaatc agttgaaacc aaacctattt 480tcccccacac ctcacggtat tgtttcgcat tccaagtttg aaacacgact ggaaacaaaa 540cccaaaacga ctggagggac cgagcttgtg ctgagcagca gagatggcgg gaaatgctgc 600gtctcccgcc tcagtttcgg atgccccgcc ctttcccaaa ccggccaccg ccgccgcccg 660tgtctcccca ccgacaggtg ggtccaatcc ttaaccacgg accagggccc ccacctgtca 720ggtggacctt ccgaagcaag gatcggccag gcgggaaaac atttcgcggc aggtggcggt 780tgcgccaaat ttctccctcc cttttccgtt cggcgtcccc aaacgcctcc ctattaatct 840ccccgcgttc cccttccctc ...
The Schizosaccharomyces pombe inv1+ regulatory region is unusually large and contains redundant cis-acting elements that function in a SAGA- and Swi/Snf-dependent fashion ...
J:74490 Degenhardt K, Rentschler S, Fishman G, Sassoon DA, Cellular and cis-regulation of En-2 expression in the mandibular arch. Mech Dev. 2002 Feb;111(1-2):125-36 ...
The N attribute of this Cell element must be one of a limited set of values that correspond to ShapeSheet cells. Refer to the table below to determine the values of the N attribute that are permitted for this Cell element.. ...